fixed up argstr of out_file

Author: tclose

pydra/tasks/mrtrix3/utils.py

@@ -25,8 +25,10 @@
         (
             "out_file",
             attr.ib(
-                type=File,
+                type=ty.Union[Path, str],
                 metadata={
+                    "position": -1,
+                    "argstr": "",
                     "help_string": "output image",
                     "output_file_template": "{in_file}_converted",
                 },
@@ -132,13 +134,36 @@ class MRConvert(ShellCommandTask):
     """
     Example
     ------
+
+    Convert NIfTI file with FSL-style gradient encoding files to
+    MRtrix Image Format with MRtrix-style gradient encoding files
+
     >>> task = MRConvert()
     >>> task.inputs.in_file = "test_dwi.nii.gz"
     >>> task.inputs.grad_fsl = ["test.bvec", "test.bval"]
     >>> task.inputs.export_grad = "test.b"
     >>> task.inputs.out_file = "test.mif"
     >>> task.cmdline
     'mrconvert test_dwi.nii.gz -fslgrad test.bvec test.bval -export_grad_mrtrix test.b test.mif'
+
+    Select the first volume from a diffusion-weighted dataset
+
+    >>> task = MRConvert()
+    >>> task.inputs.in_file = "test_dwi.nii.gz"
+    >>> task.inputs.out_file = "test_vol.nii.gz"
+    >>> task.inputs.coord = [3, 0]
+    >>> task.cmdline
+    'mrconvert test_dwi.nii.gz -coord 3 0 test_vol.nii.gz'
+
+    Extend a 3D image to 4D by adding a singular dimension
+
+    >>> task = MRConvert()
+    >>> task.inputs.in_file = "test.nii.gz"
+    >>> task.inputs.out_file = "test_set.nii.gz"
+    >>> task.inputs.axes = [0, 1, 2, -1]
+    >>> task.cmdline
+    'mrconvert test.nii.gz -axes 0,1,2,-1 test_set.nii.gz'
+
     """
 
     input_spec = MRConvertInputSpec

setup.cfg

@@ -62,3 +62,8 @@ versionfile_source = pydra/tasks/mrtrix3/_version.py
 versionfile_build = pydra/tasks/mrtrix3/_version.py
 tag_prefix =
 parentdir_prefix =
+
+
+[tool:pytest]
+addopts          = --doctest-modules --doctest-report ndiff
+doctest_optionflags= NORMALIZE_WHITESPACE ELLIPSIS