black

capsul/dataset.py

@@ -1247,8 +1247,7 @@ def path_for_parameters(self, executable, parameters=None):
 
         if parameters is None:
             parameters = [
-                field.name
-                for field in executable.user_fields()  # if field.path_type
+                field.name for field in executable.user_fields()  # if field.path_type
             ]
         if self.debug:
             if self._current_iteration is not None:

capsul/execution_context.py

@@ -760,9 +760,9 @@ def find_temporary_to_generate(executable):
             else:
                 field.generate_temporary = True
             if isinstance(node, ProcessIteration):
-                node.process.field(
-                    field.name
-                ).generate_temporary = field.generate_temporary
+                node.process.field(field.name).generate_temporary = (
+                    field.generate_temporary
+                )
             # print('!temporaries!  ', field.name, '=', field.generate_temporary)
 
     stack = [(executable, field) for field in executable.user_fields()]

capsul/pipeline/pipeline_nodes.py

@@ -385,9 +385,7 @@ def configure_controller(cls):
     def configured_controller(self):
         c = self.configure_controller()
         c.outputs = [
-            field.name
-            for field in self.fields()
-            if field.is_output()  # noqa: F811
+            field.name for field in self.fields() if field.is_output()  # noqa: F811
         ]
         c.inputs = self.get_switch_inputs()
         c.output_types = [self.field(p).type_str() for p in self.outputs]

capsul/pipeline/test/fake_morphologist/brainorientation.py

@@ -399,7 +399,9 @@ def pipeline_definition(self):
         self.Normalization_NormalizeFSL_allow_retry_initialization = True
         self.Normalization_NormalizeFSL_NormalizeFSL_cost_function = "corratio"
         self.Normalization_NormalizeFSL_NormalizeFSL_search_cost_function = "corratio"
-        self.Normalization_NormalizeFSL_ConvertFSLnormalizationToAIMS_standard_template = 0
+        self.Normalization_NormalizeFSL_ConvertFSLnormalizationToAIMS_standard_template = (
+            0
+        )
         self.Normalization_NormalizeSPM_allow_retry_initialization = True
         self.Normalization_NormalizeSPM_voxel_size = "[1 1 1]"
         self.Normalization_NormalizeSPM_cutoff_option = 25

capsul/pipeline/test/fake_morphologist/morphologist.py

@@ -1875,18 +1875,30 @@ def pipeline_definition(self):
         self.PrepareSubject_Normalization_NormalizeFSL_alignment = (
             "Not Aligned but Same Orientation"
         )
-        self.PrepareSubject_Normalization_NormalizeFSL_set_transformation_in_source_volume = True
+        self.PrepareSubject_Normalization_NormalizeFSL_set_transformation_in_source_volume = (
+            True
+        )
         self.PrepareSubject_Normalization_NormalizeFSL_NormalizeFSL_cost_function = (
             "corratio"
         )
-        self.PrepareSubject_Normalization_NormalizeFSL_NormalizeFSL_search_cost_function = "corratio"
-        self.PrepareSubject_Normalization_NormalizeFSL_ConvertFSLnormalizationToAIMS_standard_template = 0
+        self.PrepareSubject_Normalization_NormalizeFSL_NormalizeFSL_search_cost_function = (
+            "corratio"
+        )
+        self.PrepareSubject_Normalization_NormalizeFSL_ConvertFSLnormalizationToAIMS_standard_template = (
+            0
+        )
         self.PrepareSubject_Normalization_NormalizeSPM_voxel_size = "[1 1 1]"
         self.PrepareSubject_Normalization_NormalizeSPM_cutoff_option = 25
         self.PrepareSubject_Normalization_NormalizeSPM_nbiteration = 16
-        self.PrepareSubject_Normalization_NormalizeSPM_ConvertSPMnormalizationToAIMS_target = "MNI template"
-        self.PrepareSubject_Normalization_NormalizeSPM_ConvertSPMnormalizationToAIMS_removeSource = False
-        self.PrepareSubject_Normalization_NormalizeBaladin_set_transformation_in_source_volume = True
+        self.PrepareSubject_Normalization_NormalizeSPM_ConvertSPMnormalizationToAIMS_target = (
+            "MNI template"
+        )
+        self.PrepareSubject_Normalization_NormalizeSPM_ConvertSPMnormalizationToAIMS_removeSource = (
+            False
+        )
+        self.PrepareSubject_Normalization_NormalizeBaladin_set_transformation_in_source_volume = (
+            True
+        )
         self.PrepareSubject_Normalization_Normalization_AimsMIRegister_anatomical_template = "/casa/host/build/share/brainvisa-share-5.2/anatomical_templates/MNI152_T1_2mm.nii.gz"
         self.PrepareSubject_Normalization_Normalization_AimsMIRegister_mni_to_acpc = "/casa/host/build/share/brainvisa-share-5.2/transformation/talairach_TO_spm_template_novoxels.trm"
         self.PrepareSubject_Normalization_Normalization_AimsMIRegister_smoothing = 1.0
@@ -1929,15 +1941,21 @@ def pipeline_definition(self):
         self.Renorm_Normalization_NormalizeFSL_NormalizeFSL_search_cost_function = (
             "corratio"
         )
-        self.Renorm_Normalization_NormalizeFSL_ConvertFSLnormalizationToAIMS_standard_template = 0
+        self.Renorm_Normalization_NormalizeFSL_ConvertFSLnormalizationToAIMS_standard_template = (
+            0
+        )
         self.Renorm_Normalization_NormalizeSPM_voxel_size = "[1 1 1]"
         self.Renorm_Normalization_NormalizeSPM_cutoff_option = 25
         self.Renorm_Normalization_NormalizeSPM_nbiteration = 16
         self.Renorm_Normalization_NormalizeSPM_ConvertSPMnormalizationToAIMS_target = (
             "MNI template"
         )
-        self.Renorm_Normalization_NormalizeSPM_ConvertSPMnormalizationToAIMS_removeSource = False
-        self.Renorm_Normalization_NormalizeBaladin_set_transformation_in_source_volume = True
+        self.Renorm_Normalization_NormalizeSPM_ConvertSPMnormalizationToAIMS_removeSource = (
+            False
+        )
+        self.Renorm_Normalization_NormalizeBaladin_set_transformation_in_source_volume = (
+            True
+        )
         self.Renorm_Normalization_Normalization_AimsMIRegister_mni_to_acpc = "/casa/host/build/share/brainvisa-share-5.2/transformation/talairach_TO_spm_template_novoxels.trm"
         self.Renorm_Normalization_Normalization_AimsMIRegister_smoothing = 1.0
         self.SplitBrain_use_ridges = True

capsul/pipeline/test/fake_morphologist/normalizationskullstripped.py

@@ -19,9 +19,9 @@ def pipeline_definition(self):
 
         self.nodes["Normalization"].plugs["reoriented_t1mri"].optional = True
 
-        self.nodes[
-            "Normalization"
-        ].Normalization_AimsMIRegister_anatomical_template = undefined
+        self.nodes["Normalization"].Normalization_AimsMIRegister_anatomical_template = (
+            undefined
+        )
         self.nodes["Normalization"].nodes[
             "Normalization_AimsMIRegister"
         ].anatomical_template = undefined
@@ -345,7 +345,9 @@ def pipeline_definition(self):
         self.Normalization_NormalizeFSL_allow_retry_initialization = True
         self.Normalization_NormalizeFSL_NormalizeFSL_cost_function = "corratio"
         self.Normalization_NormalizeFSL_NormalizeFSL_search_cost_function = "corratio"
-        self.Normalization_NormalizeFSL_ConvertFSLnormalizationToAIMS_standard_template = 0
+        self.Normalization_NormalizeFSL_ConvertFSLnormalizationToAIMS_standard_template = (
+            0
+        )
         self.Normalization_NormalizeSPM_allow_retry_initialization = True
         self.Normalization_NormalizeSPM_voxel_size = "[1 1 1]"
         self.Normalization_NormalizeSPM_cutoff_option = 25

capsul/process/test/test_load_from_description.py

@@ -84,9 +84,9 @@ def mask(
     pass
 
 
-def cat(value1: str, value2: str, value3: str) -> field(
-    type_=str, desc="Concatenation of non empty input values."
-):
+def cat(
+    value1: str, value2: str, value3: str
+) -> field(type_=str, desc="Concatenation of non empty input values."):
     return "_".join(i for i in (value1, value2, value3) if i)