fix: specs

Author: satra

nipype/interfaces/afni/preprocess.py

@@ -2831,7 +2831,7 @@ class QwarpInputSpec(AFNICommandInputSpec):
         desc='add extra options to the 3dAllineate command to be run by '
         '3dQwarp.',
         argstr='-allineate_opts %s',
-        xand=['allineate'])
+        requires=['allineate'])
     nowarp = traits.Bool(desc='Do not save the _WARP file.', argstr='-nowarp')
     iwarp = traits.Bool(
         desc='Do compute and save the _WARPINV file.',

nipype/interfaces/afni/tests/test_auto_CatMatvec.py

@@ -12,8 +12,6 @@ def test_CatMatvec_inputs():
         ),
         fourxfour=dict(
             argstr='-4x4',
-            descr=
-            'Output matrix in augmented form (last row is 0 0 0 1)This option does not work with -MATRIX or -ONELINE',
             xor=['matrix', 'oneline'],
         ),
         ignore_exception=dict(
@@ -23,14 +21,11 @@ def test_CatMatvec_inputs():
         ),
         in_file=dict(
             argstr='%s',
-            descr='list of tuples of mfiles and associated opkeys',
             mandatory=True,
             position=-2,
         ),
         matrix=dict(
             argstr='-MATRIX',
-            descr=
-            "indicates that the resulting matrix willbe written to outfile in the 'MATRIX(...)' format (FORM 3).This feature could be used, with clever scripting, to inputa matrix directly on the command line to program 3dWarp.",
             xor=['oneline', 'fourxfour'],
         ),
         num_threads=dict(
@@ -39,13 +34,10 @@ def test_CatMatvec_inputs():
         ),
         oneline=dict(
             argstr='-ONELINE',
-            descr=
-            'indicates that the resulting matrixwill simply be written as 12 numbers on one line.',
             xor=['matrix', 'fourxfour'],
         ),
         out_file=dict(
             argstr=' > %s',
-            descr='File to write concattenated matvecs to',
             mandatory=True,
             position=-1,
         ),

nipype/interfaces/afni/tests/test_auto_CenterMass.py

@@ -10,7 +10,6 @@ def test_CenterMass_inputs():
         automask=dict(argstr='-automask', ),
         cm_file=dict(
             argstr='> %s',
-            descr='File to write center of mass to',
             hash_files=False,
             keep_extension=False,
             name_source='in_file',

nipype/interfaces/afni/tests/test_auto_NwarpCat.py

@@ -18,7 +18,6 @@ def test_NwarpCat_inputs():
         ),
         in_files=dict(
             argstr='%s',
-            descr='list of tuples of 3D warps and associated functions',
             mandatory=True,
             position=-1,
         ),

nipype/interfaces/afni/tests/test_auto_Qwarp.py

@@ -10,7 +10,7 @@ def test_Qwarp_inputs():
         allineate=dict(argstr='-allineate', ),
         allineate_opts=dict(
             argstr='-allineate_opts %s',
-            xand=['allineate'],
+            requires=['allineate'],
         ),
         allsave=dict(
             argstr='-allsave',

nipype/interfaces/afni/utils.py

@@ -564,29 +564,29 @@ class Cat(AFNICommand):
 class CatMatvecInputSpec(AFNICommandInputSpec):
     in_file = traits.List(
         traits.Tuple(traits.Str(), traits.Str()),
-        descr="list of tuples of mfiles and associated opkeys",
+        desc="list of tuples of mfiles and associated opkeys",
         mandatory=True,
         argstr="%s",
         position=-2)
     out_file = File(
-        descr="File to write concattenated matvecs to",
+        desc="File to write concattenated matvecs to",
         argstr=" > %s",
         position=-1,
         mandatory=True)
     matrix = traits.Bool(
-        descr="indicates that the resulting matrix will"
+        desc="indicates that the resulting matrix will"
         "be written to outfile in the 'MATRIX(...)' format (FORM 3)."
         "This feature could be used, with clever scripting, to input"
         "a matrix directly on the command line to program 3dWarp.",
         argstr="-MATRIX",
         xor=['oneline', 'fourxfour'])
     oneline = traits.Bool(
-        descr="indicates that the resulting matrix"
+        desc="indicates that the resulting matrix"
         "will simply be written as 12 numbers on one line.",
         argstr="-ONELINE",
         xor=['matrix', 'fourxfour'])
     fourxfour = traits.Bool(
-        descr="Output matrix in augmented form (last row is 0 0 0 1)"
+        desc="Output matrix in augmented form (last row is 0 0 0 1)"
         "This option does not work with -MATRIX or -ONELINE",
         argstr="-4x4",
         xor=['matrix', 'oneline'])
@@ -635,7 +635,7 @@ class CenterMassInputSpec(CommandLineInputSpec):
         name_template='%s_cm.out',
         hash_files=False,
         keep_extension=False,
-        descr="File to write center of mass to",
+        desc="File to write center of mass to",
         argstr="> %s",
         position=-1)
     mask_file = File(
@@ -1553,7 +1553,7 @@ class NwarpCatInputSpec(AFNICommandInputSpec):
                       traits.Tuple(
                           traits.Enum('IDENT', 'INV', 'SQRT', 'SQRTINV'),
                           traits.File())),
-        descr="list of tuples of 3D warps and associated functions",
+        desc="list of tuples of 3D warps and associated functions",
         mandatory=True,
         argstr="%s",
         position=-1)

nipype/interfaces/ants/registration.py

@@ -311,8 +311,8 @@ class RegistrationInputSpec(ANTSCommandInputSpec):
     )
 
     initial_moving_transform = InputMultiPath(
+        File(exists=True),
         argstr='%s',
-        exists=True,
         desc='A transform or a list of transforms that should be applied'
         'before the registration begins. Note that, when a list is given,'
         'the transformations are applied in reverse order.',

nipype/interfaces/ants/tests/test_auto_ComposeMultiTransform.py

@@ -26,7 +26,7 @@ def test_ComposeMultiTransform_inputs():
         ),
         output_transform=dict(
             argstr='%s',
-            keep_ext=True,
+            keep_extension=True,
             name_source=['transforms'],
             name_template='%s_composed',
             position=1,

nipype/interfaces/ants/utils.py

@@ -331,7 +331,7 @@ class ComposeMultiTransformInputSpec(ANTSCommandInputSpec):
         position=1,
         name_source=['transforms'],
         name_template='%s_composed',
-        keep_ext=True,
+        keep_extension=True,
         desc='the name of the resulting transform.')
     reference_image = File(
         argstr='%s',