Merge pull request #824 from satra/fix/misc

Fix/misc

Author: satra

nipype/interfaces/base.py

@@ -731,6 +731,7 @@ def _get_trait_desc(self, inputs, name, spec):
         desc = spec.desc
         xor = spec.xor
         requires = spec.requires
+        argstr = spec.argstr
 
         manhelpstr = ['\t%s' % name]
 
@@ -753,6 +754,17 @@ def _get_trait_desc(self, inputs, name, spec):
                                    initial_indent='\t\t',
                                    subsequent_indent='\t\t')
 
+        if argstr:
+            pos = spec.position
+            if pos is not None:
+                manhelpstr += wrap('flag: %s, position: %s' % (argstr, pos), 70,
+                                   initial_indent='\t\t',
+                                   subsequent_indent='\t\t')
+            else:
+                manhelpstr += wrap('flag: %s' % argstr, 70,
+                                   initial_indent='\t\t',
+                                   subsequent_indent='\t\t')
+
         if xor:
             line = '%s' % ', '.join(xor)
             manhelpstr += wrap(line, 70,

nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py

@@ -56,14 +56,18 @@ def test_ProcStreamlines_inputs():
     position=-1,
     ),
     outputacm=dict(argstr='-outputacm',
+    requires=['outputroot', 'seedfile'],
     ),
     outputcbs=dict(argstr='-outputcbs',
+    requires=['outputroot', 'targetfile', 'seedfile'],
     ),
     outputcp=dict(argstr='-outputcp',
+    requires=['outputroot', 'seedfile'],
     ),
     outputroot=dict(argstr='-outputroot %s',
     ),
     outputsc=dict(argstr='-outputsc',
+    requires=['outputroot', 'seedfile'],
     ),
     outputtracts=dict(argstr='-outputtracts',
     ),
@@ -103,7 +107,8 @@ def test_ProcStreamlines_inputs():
             yield assert_equal, getattr(inputs.traits()[key], metakey), value
 
 def test_ProcStreamlines_outputs():
-    output_map = dict(proc=dict(),
+    output_map = dict(outputroot_files=dict(),
+    proc=dict(),
     )
     outputs = ProcStreamlines.output_spec()
 

nipype/interfaces/fsl/tests/test_auto_DTIFit.py

@@ -17,7 +17,7 @@ def test_DTIFit_inputs():
     mandatory=True,
     position=3,
     ),
-    cni=dict(argstr='-cni %s',
+    cni=dict(argstr='--cni=%s',
     ),
     dwi=dict(argstr='-k %s',
     mandatory=True,

nipype/interfaces/fsl/tests/test_auto_Eddy.py

@@ -33,7 +33,12 @@ def test_Eddy_inputs():
     in_mask=dict(argstr='--mask=%s',
     mandatory=True,
     ),
-    in_topup=dict(argstr='--topup=%s',
+    in_topup_fieldcoef=dict(argstr='--topup=%s',
+    copyfile=False,
+    requires=['in_topup_movpar'],
+    ),
+    in_topup_movpar=dict(copyfile=False,
+    requires=['in_topup_fieldcoef'],
     ),
     method=dict(argstr='--resamp=%s',
     ),

nipype/interfaces/fsl/tests/test_auto_FIRST.py

@@ -18,6 +18,7 @@ def test_FIRST_inputs():
     usedefault=True,
     ),
     in_file=dict(argstr='-i %s',
+    copyfile=False,
     mandatory=True,
     position=-2,
     ),

nipype/interfaces/fsl/tests/test_auto_MELODIC.py

@@ -32,6 +32,7 @@ def test_MELODIC_inputs():
     in_files=dict(argstr='-i %s',
     mandatory=True,
     position=0,
+    sep=',',
     ),
     log_power=dict(argstr='--logPower',
     ),

nipype/interfaces/fsl/tests/test_auto_XFibres.py

@@ -29,6 +29,8 @@ def test_XFibres_inputs():
     ),
     fudge=dict(argstr='--fudge=%d',
     ),
+    gradnonlin=dict(argstr='--gradnonlin=%s',
+    ),
     ignore_exception=dict(nohash=True,
     usedefault=True,
     ),

nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py

@@ -16,12 +16,13 @@ def test_DiffusionTensorStreamlineTrack_inputs():
     usedefault=True,
     ),
     exclude_file=dict(argstr='-exclude %s',
-    position=2,
+    xor=['exclude_file', 'exclude_spec'],
     ),
-    exclude_spec=dict(argstr='-seed %s',
+    exclude_spec=dict(argstr='-exclude %s',
     position=2,
     sep=',',
     units='mm',
+    xor=['exclude_file', 'exclude_spec'],
     ),
     gradient_encoding_file=dict(argstr='-grad %s',
     mandatory=True,
@@ -35,12 +36,13 @@ def test_DiffusionTensorStreamlineTrack_inputs():
     position=-2,
     ),
     include_file=dict(argstr='-include %s',
-    position=2,
+    xor=['include_file', 'include_spec'],
     ),
-    include_spec=dict(argstr='-seed %s',
+    include_spec=dict(argstr='-include %s',
     position=2,
     sep=',',
     units='mm',
+    xor=['include_file', 'include_spec'],
     ),
     initial_cutoff_value=dict(argstr='-initcutoff %s',
     units='NA',
@@ -52,13 +54,14 @@ def test_DiffusionTensorStreamlineTrack_inputs():
     position=-3,
     usedefault=True,
     ),
-    mask_file=dict(argstr='-exclude %s',
-    position=2,
+    mask_file=dict(argstr='-mask %s',
+    xor=['mask_file', 'mask_spec'],
     ),
-    mask_spec=dict(argstr='-seed %s',
+    mask_spec=dict(argstr='-mask %s',
     position=2,
     sep=',',
     units='mm',
+    xor=['mask_file', 'mask_spec'],
     ),
     maximum_number_of_tracks=dict(argstr='-maxnum %d',
     ),
@@ -74,21 +77,24 @@ def test_DiffusionTensorStreamlineTrack_inputs():
     no_mask_interpolation=dict(argstr='-nomaskinterp',
     ),
     out_file=dict(argstr='%s',
-    genfile=True,
+    name_source=['in_file'],
+    name_template='%s_tracked.tck',
+    output_name='tracked.tck',
     position=-1,
     ),
     seed_file=dict(argstr='-seed %s',
-    position=2,
+    xor=['seed_file', 'seed_spec'],
     ),
     seed_spec=dict(argstr='-seed %s',
     position=2,
     sep=',',
     units='mm',
+    xor=['seed_file', 'seed_spec'],
     ),
     step_size=dict(argstr='-step %s',
     units='mm',
     ),
-    stop=dict(argstr='-gzip',
+    stop=dict(argstr='-stop',
     ),
     terminal_output=dict(mandatory=True,
     nohash=True,

nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py

@@ -16,12 +16,13 @@ def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_inputs():
     usedefault=True,
     ),
     exclude_file=dict(argstr='-exclude %s',
-    position=2,
+    xor=['exclude_file', 'exclude_spec'],
     ),
-    exclude_spec=dict(argstr='-seed %s',
+    exclude_spec=dict(argstr='-exclude %s',
     position=2,
     sep=',',
     units='mm',
+    xor=['exclude_file', 'exclude_spec'],
     ),
     ignore_exception=dict(nohash=True,
     usedefault=True,
@@ -31,12 +32,13 @@ def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_inputs():
     position=-2,
     ),
     include_file=dict(argstr='-include %s',
-    position=2,
+    xor=['include_file', 'include_spec'],
     ),
-    include_spec=dict(argstr='-seed %s',
+    include_spec=dict(argstr='-include %s',
     position=2,
     sep=',',
     units='mm',
+    xor=['include_file', 'include_spec'],
     ),
     initial_cutoff_value=dict(argstr='-initcutoff %s',
     units='NA',
@@ -48,13 +50,14 @@ def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_inputs():
     position=-3,
     usedefault=True,
     ),
-    mask_file=dict(argstr='-exclude %s',
-    position=2,
+    mask_file=dict(argstr='-mask %s',
+    xor=['mask_file', 'mask_spec'],
     ),
-    mask_spec=dict(argstr='-seed %s',
+    mask_spec=dict(argstr='-mask %s',
     position=2,
     sep=',',
     units='mm',
+    xor=['mask_file', 'mask_spec'],
     ),
     maximum_number_of_tracks=dict(argstr='-maxnum %d',
     ),
@@ -72,21 +75,24 @@ def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_inputs():
     no_mask_interpolation=dict(argstr='-nomaskinterp',
     ),
     out_file=dict(argstr='%s',
-    genfile=True,
+    name_source=['in_file'],
+    name_template='%s_tracked.tck',
+    output_name='tracked.tck',
     position=-1,
     ),
     seed_file=dict(argstr='-seed %s',
-    position=2,
+    xor=['seed_file', 'seed_spec'],
     ),
     seed_spec=dict(argstr='-seed %s',
     position=2,
     sep=',',
     units='mm',
+    xor=['seed_file', 'seed_spec'],
     ),
     step_size=dict(argstr='-step %s',
     units='mm',
     ),
-    stop=dict(argstr='-gzip',
+    stop=dict(argstr='-stop',
     ),
     terminal_output=dict(mandatory=True,
     nohash=True,

nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py

@@ -16,12 +16,13 @@ def test_SphericallyDeconvolutedStreamlineTrack_inputs():
     usedefault=True,
     ),
     exclude_file=dict(argstr='-exclude %s',
-    position=2,
+    xor=['exclude_file', 'exclude_spec'],
     ),
-    exclude_spec=dict(argstr='-seed %s',
+    exclude_spec=dict(argstr='-exclude %s',
     position=2,
     sep=',',
     units='mm',
+    xor=['exclude_file', 'exclude_spec'],
     ),
     ignore_exception=dict(nohash=True,
     usedefault=True,
@@ -31,12 +32,13 @@ def test_SphericallyDeconvolutedStreamlineTrack_inputs():
     position=-2,
     ),
     include_file=dict(argstr='-include %s',
-    position=2,
+    xor=['include_file', 'include_spec'],
     ),
-    include_spec=dict(argstr='-seed %s',
+    include_spec=dict(argstr='-include %s',
     position=2,
     sep=',',
     units='mm',
+    xor=['include_file', 'include_spec'],
     ),
     initial_cutoff_value=dict(argstr='-initcutoff %s',
     units='NA',
@@ -48,13 +50,14 @@ def test_SphericallyDeconvolutedStreamlineTrack_inputs():
     position=-3,
     usedefault=True,
     ),
-    mask_file=dict(argstr='-exclude %s',
-    position=2,
+    mask_file=dict(argstr='-mask %s',
+    xor=['mask_file', 'mask_spec'],
     ),
-    mask_spec=dict(argstr='-seed %s',
+    mask_spec=dict(argstr='-mask %s',
     position=2,
     sep=',',
     units='mm',
+    xor=['mask_file', 'mask_spec'],
     ),
     maximum_number_of_tracks=dict(argstr='-maxnum %d',
     ),
@@ -70,21 +73,24 @@ def test_SphericallyDeconvolutedStreamlineTrack_inputs():
     no_mask_interpolation=dict(argstr='-nomaskinterp',
     ),
     out_file=dict(argstr='%s',
-    genfile=True,
+    name_source=['in_file'],
+    name_template='%s_tracked.tck',
+    output_name='tracked.tck',
     position=-1,
     ),
     seed_file=dict(argstr='-seed %s',
-    position=2,
+    xor=['seed_file', 'seed_spec'],
     ),
     seed_spec=dict(argstr='-seed %s',
     position=2,
     sep=',',
     units='mm',
+    xor=['seed_file', 'seed_spec'],
     ),
     step_size=dict(argstr='-step %s',
     units='mm',
     ),
-    stop=dict(argstr='-gzip',
+    stop=dict(argstr='-stop',
     ),
     terminal_output=dict(mandatory=True,
     nohash=True,