merge conflicts

Author: yibeichan

pydra/tasks/fsl/utils/convertxfm.py

@@ -87,9 +87,7 @@ def ConvertXFM_output(inputs):
         },
     ),
 ]
-ConvertXFM_input_spec = specs.SpecInfo(
-    name="Input", fields=input_fields, bases=(specs.ShellSpec,)
-)
+ConvertXFM_input_spec = specs.SpecInfo(name="Input", fields=input_fields, bases=(specs.ShellSpec,))
 
 output_fields = []
 ConvertXFM_output_spec = specs.SpecInfo(

pydra/tasks/fsl/utils/tests/test_run_convertxfm.py

@@ -3,9 +3,7 @@
 from ..convertxfm import ConvertXFM
 
 
-@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", [({"in_file": "flirt.mat", "invert_xfm": True}, ["out_file"])]
 )
@@ -35,9 +33,7 @@ def test_ConvertXFM(test_data, inputs, outputs):
             except:
                 pass
         task = ConvertXFM(**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/utils/tests/test_spec_convertxfm.py

@@ -32,6 +32,4 @@ def test_ConvertXFM(test_data, inputs, outputs):
             except:
                 pass
         task = ConvertXFM(**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)

specs/callables.py

@@ -133,7 +133,6 @@ def FAST_output_infile(field, in_files, out_basename):
         outputs.append(f"{out_basename}_{suffix}")
     return outputs
 
-
 def FEAT_output(fsf_file):
     is_ica = False
     with open(fsf_file, "rt") as fp:
@@ -384,4 +383,5 @@ def SLICE_output(inputs):
     else:
         fname_template = f"{inputs.in_file}_{suffix}"
 
-    return sorted(glob(fname_template))
+    return sorted(glob(fname_template))
+

tools/converter.py

@@ -202,7 +202,7 @@ def write_test(self, filename_test, run=False):
         spec_str += f"    if inputs is None:\n"
         spec_str += f"        in_file = Path(test_data) / 'test.nii.gz'\n"
         spec_str += f"        task = {self.interface_name}(in_file=in_file)\n"
-        spec_str += f"    else:\n" 
+        spec_str += f"    else:\n"
         spec_str += f"        for key, val in inputs.items():\n"
         spec_str += f"            try:  \n"
         spec_str += f"                pattern = r'\.[a-zA-Z]*'\n"
@@ -253,7 +253,7 @@ def write_test_error(self, input_error):
         spec_str += f"    if inputs is None:\n"
         spec_str += f"        in_file = Path(test_data) / 'test.nii.gz'\n"
         spec_str += f"        task = {self.interface_name}(in_file=in_file)\n"
-        spec_str += f"    else:\n" 
+        spec_str += f"    else:\n"
         spec_str += f"        for key, val in inputs.items():\n"
         spec_str += f"            try:  \n"
         spec_str += f"                pattern = r'\.[a-zA-Z]*'\n"