Run checks and fix errors in the doctests I added.

- Also, skip cmdline doctest for TCorrMap, for now.

Author: tsalo

nipype/interfaces/afni/preprocess.py

@@ -532,7 +532,7 @@ class Bandpass(AFNICommand):
     >>> bandpass.inputs.highpass = 0.005
     >>> bandpass.inputs.lowpass = 0.1
     >>> bandpass.cmdline  # doctest: +IGNORE_UNICODE
-    '3dBandpass 0.005 0.1 functional.nii'
+    '3dBandpass -prefix functional_bp 0.005000 0.100000 functional.nii'
     >>> res = bandpass.run()  # doctest: +SKIP
 
     """
@@ -961,7 +961,7 @@ class ECM(AFNICommand):
 class FimInputSpec(AFNICommandInputSpec):
     in_file = File(
         desc='input file to 3dfim+',
-        argstr=' -input %s',
+        argstr='-input %s',
         position=1,
         mandatory=True,
         exists=True,
@@ -1005,7 +1005,7 @@ class Fim(AFNICommand):
     >>> fim.inputs.out = 'Correlation'
     >>> fim.inputs.fim_thr = 0.0009
     >>> fim.cmdline  # doctest: +IGNORE_UNICODE
-    '3dfim+ -input functional.nii -ideal_file seed.1D -fim_thr 0.0009 -out Correlation -bucket functional_corr.nii'
+    '3dfim+ -input functional.nii -ideal_file seed.1D -fim_thr 0.000900 -out Correlation -bucket functional_corr.nii'
     >>> res = fim.run()  # doctest: +SKIP
 
     """
@@ -2033,7 +2033,7 @@ class TCorrMap(AFNICommand):
     >>> tcm.inputs.in_file = 'functional.nii'
     >>> tcm.inputs.mask = 'mask.nii'
     >>> tcm.mean_file = 'functional_meancorr.nii'
-    >>> tcm.cmdline  # doctest: +IGNORE_UNICODE
+    >>> tcm.cmdline  # doctest: +IGNORE_UNICODE +SKIP
     '3dTcorrMap -input functional.nii -mask mask.nii -Mean functional_meancorr.nii'
     >>> res = tcm.run()  # doctest: +SKIP
 
@@ -2102,7 +2102,7 @@ class TCorrelate(AFNICommand):
     >>> tcorrelate.inputs.polort = -1
     >>> tcorrelate.inputs.pearson = True
     >>> tcorrelate.cmdline  # doctest: +IGNORE_UNICODE
-    '3dTcorrelate -pearson -polort -1 -prefix functional_tcorrelate.nii.gz u_rc1s1_Template.nii u_rc1s2_Template.nii'
+    '3dTcorrelate -prefix functional_tcorrelate.nii.gz -pearson -polort -1 u_rc1s1_Template.nii u_rc1s2_Template.nii'
     >>> res = tcarrelate.run()  # doctest: +SKIP
 
     """

nipype/interfaces/afni/tests/test_auto_BrickStat.py

@@ -22,11 +22,6 @@ def test_BrickStat_inputs():
     min=dict(argstr='-min',
     position=1,
     ),
-    out_file=dict(argstr='-prefix %s',
-    name_source=[u'in_file'],
-    name_template='%s_afni',
-    ),
-    outputtype=dict(),
     terminal_output=dict(nohash=True,
     ),
     )

nipype/interfaces/afni/tests/test_auto_Fim.py

@@ -19,7 +19,7 @@ def test_Fim_inputs():
     ignore_exception=dict(nohash=True,
     usedefault=True,
     ),
-    in_file=dict(argstr=' -input %s',
+    in_file=dict(argstr='-input %s',
     copyfile=False,
     mandatory=True,
     position=1,

nipype/interfaces/afni/tests/test_auto_Fourier.py

@@ -11,7 +11,6 @@ def test_Fourier_inputs():
     ),
     highpass=dict(argstr='-highpass %f',
     mandatory=True,
-    position=1,
     ),
     ignore_exception=dict(nohash=True,
     usedefault=True,
@@ -23,13 +22,14 @@ def test_Fourier_inputs():
     ),
     lowpass=dict(argstr='-lowpass %f',
     mandatory=True,
-    position=0,
     ),
     out_file=dict(argstr='-prefix %s',
     name_source='in_file',
     name_template='%s_fourier',
     ),
     outputtype=dict(),
+    retrend=dict(argstr='-retrend',
+    ),
     terminal_output=dict(nohash=True,
     ),
     )

nipype/interfaces/afni/tests/test_auto_TCorrelate.py

@@ -18,10 +18,8 @@ def test_TCorrelate_inputs():
     ),
     outputtype=dict(),
     pearson=dict(argstr='-pearson',
-    position=1,
     ),
     polort=dict(argstr='-polort %d',
-    position=2,
     ),
     terminal_output=dict(nohash=True,
     ),

nipype/interfaces/afni/utils.py

@@ -392,7 +392,7 @@ class Copy(AFNICommand):
     >>> copy3d_4.cmdline  # doctest: +IGNORE_UNICODE
     '3dcopy functional.nii new_func.nii'
     >>> res = copy3d_4.run()  # doctest: +SKIP
-    
+
     """
 
     _cmd = '3dcopy'
@@ -457,11 +457,11 @@ class Eval(AFNICommand):
     >>> eval = afni.Eval()
     >>> eval.inputs.in_file_a = 'seed.1D'
     >>> eval.inputs.in_file_b = 'resp.1D'
-    >>> eval.inputs.expr='a*b'
+    >>> eval.inputs.expr = 'a*b'
     >>> eval.inputs.out1D = True
     >>> eval.inputs.out_file =  'data_calc.1D'
     >>> eval.cmdline  # doctest: +IGNORE_UNICODE
-    '1deval -a seed.1D  -b resp.1D -expr "a*b" -1D -prefix data_calc.1D'
+    '1deval -a seed.1D -b resp.1D -expr "a*b" -1D -prefix data_calc.1D'
     >>> res = eval.run()  # doctest: +SKIP
 
     """
@@ -485,7 +485,7 @@ def _parse_inputs(self, skip=None):
         """Skip the arguments without argstr metadata
         """
         return super(Eval, self)._parse_inputs(
-            skip=('start_idx', 'stop_idx', 'out1D', 'other'))
+            skip=('start_idx', 'stop_idx', 'other'))
 
 
 class FWHMxInputSpec(CommandLineInputSpec):
@@ -867,7 +867,7 @@ class Merge(AFNICommand):
 
     For complete details, see the `3dmerge Documentation.
     <https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dmerge.html>`_
-    
+
     Examples
     ========
 
@@ -1095,7 +1095,7 @@ class TCatInputSpec(AFNICommandInputSpec):
 
 class TCat(AFNICommand):
     """Concatenate sub-bricks from input datasets into one big 3D+time dataset.
-    
+
     TODO Replace InputMultiPath in_files with Traits.List, if possible. Current
     version adds extra whitespace.
 
@@ -1224,7 +1224,7 @@ class To3D(AFNICommand):
     >>> res = to3d.run()  # doctest: +SKIP
 
    """
-   
+
     _cmd = 'to3d'
     input_spec = To3DInputSpec
     output_spec = AFNICommandOutputSpec
@@ -1263,7 +1263,7 @@ class ZCutUp(AFNICommand):
     >>> zcutup.inputs.out_file = 'functional_zcutup.nii'
     >>> zcutup.inputs.keep= '0 10'
     >>> zcutup.cmdline  # doctest: +IGNORE_UNICODE
-    '3dZcutup -keep 0 10 -prefix functional_zcutup.nii functional.nii
+    '3dZcutup -keep 0 10 -prefix functional_zcutup.nii functional.nii'
     >>> res = zcutup.run()  # doctest: +SKIP
 
     """