Merge branch 'wip-yc-convert' of github.com:yibeichan/pydra-fsl into wip-yc-convert

Author: yibeichan

pydra/tasks/fsl/model/cluster.py

@@ -221,9 +221,7 @@ def Cluster_output(field, inputs):
         },
     ),
 ]
-Cluster_input_spec = specs.SpecInfo(
-    name="Input", fields=input_fields, bases=(specs.ShellSpec,)
-)
+Cluster_input_spec = specs.SpecInfo(name="Input", fields=input_fields, bases=(specs.ShellSpec,))
 
 output_fields = [
     (

pydra/tasks/fsl/model/tests/test_run_cluster.py

@@ -3,9 +3,7 @@
 from ..cluster import Cluster
 
 
-@pytest.mark.xfail(
-    "FSLDIR" not in os.environ, reason="no FSL found", raises=FileNotFoundError
-)
+@pytest.mark.xfail("FSLDIR" not in os.environ, reason="no FSL found", raises=FileNotFoundError)
 @pytest.mark.parametrize(
     "inputs, outputs",
     [
@@ -63,9 +61,7 @@ def test_Cluster(test_data, inputs, outputs):
             except:
                 pass
         task = Cluster(**inputs)
-    assert set(task.generated_output_names) == set(
-        ["return_code", "stdout", "stderr"] + outputs
-    )
+    assert set(task.generated_output_names) == set(["return_code", "stdout", "stderr"] + outputs)
     res = task()
     print("RESULT: ", res)
     for out_nm in outputs:

pydra/tasks/fsl/model/tests/test_spec_cluster.py

@@ -60,6 +60,4 @@ def test_Cluster(test_data, inputs, outputs):
             except:
                 pass
         task = Cluster(**inputs)
-    assert set(task.generated_output_names) == set(
-        ["return_code", "stdout", "stderr"] + outputs
-    )
+    assert set(task.generated_output_names) == set(["return_code", "stdout", "stderr"] + outputs)

pydra/tasks/fsl/tests/data/design.con

@@ -5,4 +5,4 @@
 /RequiredEffect     100
 
 /Matrix
-1
+1

pydra/tasks/fsl/tests/data/design.grp

@@ -27,4 +27,4 @@
 1
 1
 1
-1
+1

pydra/tasks/fsl/tests/data/design.mat

@@ -28,4 +28,4 @@
 1
 1
 1
-1
+1

specs/callables.py

@@ -5,7 +5,7 @@ def Cluster_output(field, inputs):
     in_file = inputs.in_file
     name = field.name
     pth, fname, ext = split_filename(in_file)
-    
+
     if name == "index_file":
         return os.path.join(pth, f"{fname}_index{ext}")
     elif name == "localmax_txt_file":
@@ -24,7 +24,9 @@ def Cluster_output(field, inputs):
         return os.path.join(pth, f"{fname}_threshold{ext}")
 
     else:
-        raise Exception(f"this function should be run only for index_file, localmax_txt_file, localmax_vol_file, max_file, mean_file, pval_file, size_file, or threshold_file not {name}")
+        raise Exception(
+            f"this function should be run only for index_file, localmax_txt_file, localmax_vol_file, max_file, mean_file, pval_file, size_file, or threshold_file not {name}"
+        )
 
 
 def Complex_output(inputs):

specs/fsl_model_param.yml

@@ -18,7 +18,7 @@ Cluster:
     size_file: Cluster_output
     threshold_file: Cluster_output
   output_templates:
-    
+
   inputs_drop:
   doctest:
     in_file: zstat1.nii.gz