add auto tests, fix doctests

Author: oesteban

nipype/interfaces/mrtrix3/connectivity.py

@@ -95,10 +95,10 @@ class BuildConnectome(MRTrix3Base):
 
     >>> import nipype.interfaces.mrtrix3 as mrt
     >>> mat = mrt.BuildConnectome()
-    >>> mat.inputs.in_file = 'tracked.tck'
-    >>> mat.inputs.in_parc = 'aparc+aseg.nii.gz'
+    >>> mat.inputs.in_file = 'tracks.tck'
+    >>> mat.inputs.in_parc = 'aparc+aseg.nii'
     >>> mat.cmdline                               # doctest: +ELLIPSIS
-    'tck2connectome tracked.tck aparc+aseg.nii.gz connectome.csv'
+    'tck2connectome tracks.tck aparc+aseg.nii connectome.csv'
     >>> mat.run()                                 # doctest: +SKIP
     """
 
@@ -154,10 +154,10 @@ class LabelConfig(MRTrix3Base):
 
     >>> import nipype.interfaces.mrtrix3 as mrt
     >>> labels = mrt.LabelConfig()
-    >>> labels.inputs.in_file = 'aparc+aseg.nii.gz'
+    >>> labels.inputs.in_file = 'aparc+aseg.nii'
     >>> labels.inputs.in_config = 'mrtrix3_labelconfig.txt'
     >>> labels.cmdline                               # doctest: +ELLIPSIS
-    'labelconfig aparc+aseg.nii.gz mrtrix3_labelconfig.txt parcellation.mif'
+    'labelconfig aparc+aseg.nii mrtrix3_labelconfig.txt parcellation.mif'
     >>> labels.run()                                 # doctest: +SKIP
     """
 

nipype/interfaces/mrtrix3/preprocess.py

@@ -183,11 +183,11 @@ class ReplaceFSwithFIRST(CommandLine):
 
     >>> import nipype.interfaces.mrtrix3 as mrt
     >>> prep = mrt.ReplaceFSwithFIRST()
-    >>> prep.inputs.in_file = 'aparc+aseg.nii.gz'
+    >>> prep.inputs.in_file = 'aparc+aseg.nii'
     >>> prep.inputs.in_t1w = 'T1.nii.gz'
     >>> prep.inputs.in_config = 'mrtrix3_labelconfig.txt'
     >>> prep.cmdline                               # doctest: +ELLIPSIS
-    'fs_parc_replace_sgm_first aparc+aseg.nii.gz T1.nii.gz \
+    'fs_parc_replace_sgm_first aparc+aseg.nii T1.nii.gz \
 mrtrix3_labelconfig.txt aparc+first.mif'
     >>> prep.run()                                 # doctest: +SKIP
     """

nipype/interfaces/mrtrix3/tests/test_auto_BuildConnectome.py

@@ -0,0 +1,63 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.interfaces.mrtrix3.connectivity import BuildConnectome
+
+def test_BuildConnectome_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_file=dict(argstr='%s',
+    mandatory=True,
+    position=-3,
+    ),
+    in_parc=dict(argstr='%s',
+    position=-2,
+    ),
+    in_scalar=dict(argstr='-image %s',
+    ),
+    in_weights=dict(argstr='-tck_weights_in %s',
+    ),
+    keep_unassigned=dict(argstr='-keep_unassigned',
+    ),
+    metric=dict(argstr='-metric %s',
+    ),
+    nthreads=dict(argstr='-nthreads %d',
+    ),
+    out_file=dict(argstr='%s',
+    mandatory=True,
+    position=-1,
+    usedefault=True,
+    ),
+    search_forward=dict(argstr='-assignment_forward_search %f',
+    ),
+    search_radius=dict(argstr='-assignment_radial_search %f',
+    ),
+    search_reverse=dict(argstr='-assignment_reverse_search %f',
+    ),
+    terminal_output=dict(nohash=True,
+    ),
+    vox_lookup=dict(argstr='-assignment_voxel_lookup',
+    ),
+    zero_diagonal=dict(argstr='-zero_diagonal',
+    ),
+    )
+    inputs = BuildConnectome.input_spec()
+
+    for key, metadata in input_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(inputs.traits()[key], metakey), value
+
+def test_BuildConnectome_outputs():
+    output_map = dict(out_file=dict(),
+    )
+    outputs = BuildConnectome.output_spec()
+
+    for key, metadata in output_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value
+

nipype/interfaces/mrtrix3/tests/test_auto_LabelConfig.py

@@ -0,0 +1,55 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.interfaces.mrtrix3.connectivity import LabelConfig
+
+def test_LabelConfig_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_config=dict(argstr='%s',
+    position=-2,
+    ),
+    in_file=dict(argstr='%s',
+    mandatory=True,
+    position=-3,
+    ),
+    lut_aal=dict(argstr='-lut_aal %s',
+    ),
+    lut_basic=dict(argstr='-lut_basic %s',
+    ),
+    lut_fs=dict(argstr='-lut_freesurfer %s',
+    ),
+    lut_itksnap=dict(argstr='-lut_itksnap %s',
+    ),
+    nthreads=dict(argstr='-nthreads %d',
+    ),
+    out_file=dict(argstr='%s',
+    mandatory=True,
+    position=-1,
+    usedefault=True,
+    ),
+    spine=dict(argstr='-spine %s',
+    ),
+    terminal_output=dict(nohash=True,
+    ),
+    )
+    inputs = LabelConfig.input_spec()
+
+    for key, metadata in input_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(inputs.traits()[key], metakey), value
+
+def test_LabelConfig_outputs():
+    output_map = dict(out_file=dict(),
+    )
+    outputs = LabelConfig.output_spec()
+
+    for key, metadata in output_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value
+

nipype/interfaces/mrtrix3/tests/test_auto_ReplaceFSwithFIRST.py

@@ -0,0 +1,47 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.interfaces.mrtrix3.preprocess import ReplaceFSwithFIRST
+
+def test_ReplaceFSwithFIRST_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_config=dict(argstr='%s',
+    position=-2,
+    ),
+    in_file=dict(argstr='%s',
+    mandatory=True,
+    position=-4,
+    ),
+    in_t1w=dict(argstr='%s',
+    mandatory=True,
+    position=-3,
+    ),
+    out_file=dict(argstr='%s',
+    mandatory=True,
+    position=-1,
+    usedefault=True,
+    ),
+    terminal_output=dict(nohash=True,
+    ),
+    )
+    inputs = ReplaceFSwithFIRST.input_spec()
+
+    for key, metadata in input_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(inputs.traits()[key], metakey), value
+
+def test_ReplaceFSwithFIRST_outputs():
+    output_map = dict(out_file=dict(),
+    )
+    outputs = ReplaceFSwithFIRST.output_spec()
+
+    for key, metadata in output_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value
+