[WIP] FIX - AFNI Zeropad sets out_file

nipype/interfaces/afni/tests/test_auto_Zeropad.py

@@ -70,7 +70,6 @@ def test_Zeropad_inputs():
         out_file=dict(
             argstr="-prefix %s",
             extensions=None,
-            name_template="zeropad",
         ),
         outputtype=dict(),
         z=dict(

nipype/interfaces/afni/tests/test_extra_Zeropad.py

@@ -0,0 +1,39 @@
+from pathlib import Path
+from nipype import Node
+from nipype.interfaces.afni import Zeropad
+from nipype.testing.fixtures import create_files_in_directory
+
+
+def test_zeropad_handles_outfile_default(create_files_in_directory):
+    filelist, outdir = create_files_in_directory
+    zp = Zeropad(I=1)
+    zp.inputs.in_files = filelist[0]
+
+    result = zp.run()
+
+    assert (Path(outdir) / "zeropad+tlrc.BRIK").exists()
+    assert Path(result.outputs.out_file).name == "zeropad+tlrc.BRIK"
+
+
+def test_zeropad_handles_outfile_specified_nii_gz(create_files_in_directory):
+    filelist, outdir = create_files_in_directory
+    zp = Zeropad(I=1, out_file="padded.nii.gz")
+    zp.inputs.in_files = filelist[0]
+
+    result = zp.run()
+
+    assert (Path(outdir) / "padded.nii.gz").exists()
+    assert Path(result.outputs.out_file).name == "padded.nii.gz"
+
+
+def test_zeropad_keeps_file_after_node_run(create_files_in_directory):
+    filelist, outdir = create_files_in_directory
+
+    zp = Node(
+        Zeropad(I=1, out_file="padded.nii.gz"), name="test_zeropad", base_dir=outdir
+    )
+    zp.inputs.in_files = Path(outdir) / filelist[0]
+
+    result = zp.run()
+    assert (Path(zp.output_dir()) / "padded.nii.gz").exists()
+    assert Path(result.outputs.out_file).name == "padded.nii.gz"

nipype/interfaces/afni/utils.py

@@ -3391,7 +3391,6 @@
         copyfile=False,
     )
     out_file = File(
-        name_template="zeropad",
         desc="output dataset prefix name (default 'zeropad')",
         argstr="-prefix %s",
     )
@@ -3497,3 +3496,10 @@
     _cmd = "3dZeropad"
     input_spec = ZeropadInputSpec
     output_spec = AFNICommandOutputSpec
+
+    def _list_outputs(self):
+        out_file = getattr(self.inputs, "out_file")
+
+        if not isdefined(out_file):
+            out_file = "zeropad+tlrc.BRIK"
+        return {"out_file": op.abspath(out_file)}