remove stuff form other branch, add string interpolation

Author: Zach Lindsey

nipype/interfaces/afni/tests/test_auto_Zeropad.py

@@ -70,6 +70,7 @@ 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

@@ -3,37 +3,3 @@
 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

@@ -3391,6 +3391,7 @@ class ZeropadInputSpec(AFNICommandInputSpec):
         copyfile=False,
     )
     out_file = File(
+        name_template="zeropad",
         desc="output dataset prefix name (default 'zeropad')",
         argstr="-prefix %s",
     )
@@ -3496,10 +3497,3 @@ class Zeropad(AFNICommand):
     _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)}

nipype/interfaces/utility/__init__.py

@@ -6,6 +6,6 @@
 Requires Packages to be installed
 """
 
-from .base import IdentityInterface, Rename, Select, Split, Merge, AssertEqual
+from .base import IdentityInterface, Rename, Select, Split, Merge, AssertEqual, StringInterpolate
 from .csv import CSVReader
 from .wrappers import Function

nipype/interfaces/utility/base.py

@@ -430,3 +430,26 @@ def _run_interface(self, runtime):
         if not np.array_equal(data1, data2):
             raise RuntimeError("Input images are not exactly equal")
         return runtime
+
+
+class StringInterpolateInputSpec(DynamicTraitedSpec):
+    input_string = Str(mandatory = True)
+
+class StringInterpolateOutputSpec(TraitedSpec):
+    output_string = Str()
+
+class StringInterpolate(BaseInterface):
+    input_spec = StringInterpolateInputSpec
+    output_spec = StringInterpolateOutputSpec
+
+    def _run_interface(self, runtime):
+
+        subs = {
+            k: getattr(self.inputs, k) for k,_ in self.inputs.items() if k != "input_string"
+        }
+        self._output_string = self.inputs.input_string.format(**subs)
+
+    def _list_outputs(self):
+        return {
+            "output_string": self._output_string
+        }

nipype/interfaces/utility/tests/test_auto_StringInterpolate.py

@@ -0,0 +1,26 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from ..base import StringInterpolate
+
+
+def test_StringInterpolate_inputs():
+    input_map = dict(
+        input_string=dict(
+            mandatory=True,
+        ),
+    )
+    inputs = StringInterpolate.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value
+
+
+def test_StringInterpolate_outputs():
+    output_map = dict(
+        output_string=dict(),
+    )
+    outputs = StringInterpolate.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.traits()[key], metakey) == value

nipype/interfaces/utility/tests/test_base.py

@@ -78,3 +78,16 @@ def test_merge(tmpdir, args, kwargs, in_lists, expected):
         assert not isdefined(res.outputs.out)
     else:
         assert res.outputs.out == expected
+
+
+def test_string_interpolate():
+
+    interpolate = utility.StringInterpolate()
+
+    interpolate.inputs.input_string = "{greeting}, {name}!"
+    interpolate.inputs.greeting = "Hello"
+    interpolate.inputs.name = "Nipype"
+
+    res = interpolate.run()
+
+    assert res.outputs.output_string == "Hello, Nipype!"