Merge pull request nipy#1449 from satra/rel/0.12rc1

final changes before tagging release candidate

CHANGES

@@ -1,4 +1,4 @@
-Next release
+Release 0.12.0-rc1 (April 20, 2016)
 ============
 
 * ENH: Add nipype_crash_search command (https://github.com/nipy/nipype/pull/1422)

nipype/info.py

@@ -10,7 +10,7 @@
 _version_major = 0
 _version_minor = 12
 _version_micro = 0
-_version_extra = '-dev'  # Remove -dev for release
+_version_extra = '-rc1'  # Remove -dev for release
 
 
 def get_nipype_gitversion():

nipype/interfaces/afni/preprocess.py

@@ -2178,7 +2178,7 @@ class FWHMxInputSpec(CommandLineInputSpec):
              'is not given, the program picks q=NT/30. -detrend disables -demed, and includes '
              '-unif.')
     demed = traits.Bool(
-        False, argstr='-demed', xorg=['detrend'],
+        False, argstr='-demed', xor=['detrend'],
         desc='If the input dataset has more than one sub-brick (e.g., has a time axis), then '
              'subtract the median of each voxel\'s time series before processing FWHM. This will '
              'tend to remove intrinsic spatial structure and leave behind the noise.')

nipype/interfaces/afni/tests/test_auto_FWHMx.py

@@ -20,7 +20,7 @@ def test_FWHMx_inputs():
     compat=dict(argstr='-compat',
     ),
     demed=dict(argstr='-demed',
-    xorg=['detrend'],
+    xor=['detrend'],
     ),
     detrend=dict(argstr='-detrend',
     usedefault=True,

nipype/interfaces/dipy/reconstruction.py

@@ -276,9 +276,9 @@ def _list_outputs(self):
 class CSDInputSpec(DipyBaseInterfaceInputSpec):
     in_mask = File(exists=True, desc=('input mask in which compute tensors'))
     response = File(exists=True, desc=('single fiber estimated response'))
-    sh_order = traits.Int(8, exists=True, usedefault=True,
+    sh_order = traits.Int(8, usedefault=True,
                           desc=('maximal shperical harmonics order'))
-    save_fods = traits.Bool(True, exists=True, usedefault=True,
+    save_fods = traits.Bool(True, usedefault=True,
                             desc=('save fODFs in file'))
     out_fods = File(desc=('fODFs output file name'))
 

nipype/interfaces/dipy/tests/test_auto_CSD.py

@@ -19,11 +19,9 @@ def test_CSD_inputs():
     out_fods=dict(),
     out_prefix=dict(),
     response=dict(),
-    save_fods=dict(exists=True,
-    usedefault=True,
+    save_fods=dict(usedefault=True,
     ),
-    sh_order=dict(exists=True,
-    usedefault=True,
+    sh_order=dict(usedefault=True,
     ),
     )
     inputs = CSD.input_spec()

nipype/interfaces/freesurfer/model.py

@@ -654,7 +654,7 @@ class SegStatsInputSpec(FSTraitedSpec):
     wm_vol_from_surf = traits.Bool(argstr='--surf-wm-vol', desc='Compute wm volume from surf')
     cortex_vol_from_surf = traits.Bool(argstr='--surf-ctx-vol', desc='Compute cortex volume from surf')
     non_empty_only = traits.Bool(argstr='--nonempty', desc='Only report nonempty segmentations')
-    empty = traits.Bool(argstr="--empty", mandatory=False,
+    empty = traits.Bool(argstr="--empty",
                         desc="Report on segmentations listed in the color table")
     mask_file = File(exists=True, argstr='--mask %s',
                      desc='Mask volume (same size as seg')
@@ -690,7 +690,7 @@ class SegStatsInputSpec(FSTraitedSpec):
                              desc="Compute volume of total gray matter")
     euler = traits.Bool(argstr="--euler",
                         desc="Write out number of defect holes in orig.nofix based on the euler number")
-    in_intensity = File(argstr="--in %s --in-intensity-name %s", mandatory=False,
+    in_intensity = File(argstr="--in %s --in-intensity-name %s",
                         desc="Undocumented input norm.mgz file")
     intensity_units = traits.Enum('MR', argstr="--in-intensity-units %s",
                                   requires=["in_intensity"], desc="Intensity units")
@@ -1083,14 +1083,13 @@ class Label2LabelInputSpec(FSTraitedSpec):
     source_subject = traits.String(argstr="--srcsubject %s", mandatory=True,
                                    desc="Source subject name")
     # optional
-    out_file = File(argstr="--trglabel %s", mandatory=False,
+    out_file = File(argstr="--trglabel %s",
                     name_source=['source_label'], name_template='%s_converted',
                     hash_files=False, keep_extension=True,
                     desc="Target label")
     registration_method = traits.Enum('surface', 'volume', usedefault=True,
                                         argstr="--regmethod %s", desc="Registration method")
-    copy_inputs = traits.Bool(mandatory=False,
-                              desc="If running as a node, set this to True." +
+    copy_inputs = traits.Bool(desc="If running as a node, set this to True." +
                               "This will copy the input files to the node " +
                               "directory.")
 
@@ -1180,11 +1179,11 @@ class Label2AnnotInputSpec(FSTraitedSpec):
     orig = File(exists=True, mandatory=True,
                 desc="implicit {hemisphere}.orig")
     # optional
-    keep_max = traits.Bool(argstr="--maxstatwinner", mandatory=False,
+    keep_max = traits.Bool(argstr="--maxstatwinner",
                            desc="Keep label with highest 'stat' value")
-    verbose_off = traits.Bool(argstr="--noverbose", mandatory=False,
+    verbose_off = traits.Bool(argstr="--noverbose",
                               desc="Turn off overlap and stat override messages")
-    color_table = File(argstr="--ctab %s", mandatory=False, exists=True,
+    color_table = File(argstr="--ctab %s", exists=True,
                        desc="File that defines the structure names, their indices, and their color")
     copy_inputs = traits.Bool(desc="copy implicit inputs and create a temp subjects_dir")
 

nipype/interfaces/freesurfer/preprocess.py

@@ -1502,11 +1502,11 @@ class NormalizeInputSpec(FSTraitedSpec):
     # optional
     gradient = traits.Int(1, argstr="-g %d", usedefault=False,
                           desc="use max intensity/mm gradient g (default=1)")
-    mask = File(argstr="-mask %s", mandatory=False, exists=True,
+    mask = File(argstr="-mask %s",  exists=True,
                 desc="The input mask file for Normalize")
-    segmentation = File(argstr="-aseg %s", mandatory=False,
+    segmentation = File(argstr="-aseg %s",
                         exists=True, desc="The input segmentation for Normalize")
-    transform = File(exists=True, mandatory=False,
+    transform = File(exists=True,
                      desc="Tranform file from the header of the input file")
 
 
@@ -1551,9 +1551,9 @@ class CANormalizeInputSpec(FSTraitedSpec):
     transform = File(argstr='%s', exists=True, mandatory=True,
                      position=-2, desc="The tranform file in lta format")
     # optional
-    mask = File(argstr='-mask %s', exists=True, mandatory=False,
+    mask = File(argstr='-mask %s', exists=True,
                 desc="Specifies volume to use as mask")
-    control_points = File(argstr='-c %s', mandatory=False,
+    control_points = File(argstr='-c %s',
                           desc="File name for the output control points")
     long_file = File(argstr='-long %s',
                      desc='undocumented flag used in longitudinal processing')
@@ -1596,20 +1596,20 @@ class CARegisterInputSpec(FSTraitedSpecOpenMP):
     #required
     in_file = File(argstr='%s', exists=True, mandatory=True,
                    position=-3, desc="The input volume for CARegister")
-    out_file = File(argstr='%s', mandatory=False, position=-1,
+    out_file = File(argstr='%s',  position=-1,
                     genfile=True, desc="The output volume for CARegister")
-    template = File(argstr='%s', exists=True, mandatory=False,
+    template = File(argstr='%s', exists=True,
                     position=-2, desc="The template file in gca format")
     # optional
-    mask = File(argstr='-mask %s', exists=True, mandatory=False,
+    mask = File(argstr='-mask %s', exists=True,
                 desc="Specifies volume to use as mask")
-    invert_and_save = traits.Bool(argstr='-invert-and-save', mandatory=False, position=-4,
+    invert_and_save = traits.Bool(argstr='-invert-and-save',  position=-4,
                                   desc="Invert and save the .m3z multi-dimensional talaraich transform to x, y, and z .mgz files")
     no_big_ventricles = traits.Bool(
-        argstr='-nobigventricles', mandatory=False, desc="No big ventricles")
-    transform = File(argstr='-T %s', exists=True, mandatory=False,
+        argstr='-nobigventricles',  desc="No big ventricles")
+    transform = File(argstr='-T %s', exists=True,
                      desc="Specifies transform in lta format")
-    align = traits.String(argstr='-align-%s', mandatory=False,
+    align = traits.String(argstr='-align-%s',
                           desc="Specifies when to perform alignment")
     levels = traits.Int(
         argstr='-levels %d',
@@ -1675,17 +1675,18 @@ class CALabelInputSpec(FSTraitedSpecOpenMP):
     intensities = File(argstr="-r %s", exists=True,
                        desc="input label intensities file(used in longitudinal processing)")
     no_big_ventricles = traits.Bool(
-        argstr="-nobigventricles", mandatory=False, desc="No big ventricles")
-    align = traits.Bool(argstr="-align", mandatory=False, desc="Align CALabel")
+        argstr="-nobigventricles",  desc="No big ventricles")
+    align = traits.Bool(argstr="-align",  desc="Align CALabel")
     prior = traits.Float(argstr="-prior %.1f",
-                         mandatory=False, desc="Prior for CALabel")
+                          desc="Prior for CALabel")
     relabel_unlikely = traits.Tuple(traits.Int, traits.Float,
                                     argstr="-relabel_unlikely %d %.1f",
-                                    desc="Reclassify voxels at least some std devs from the mean using some size Gaussian window",
-                                    mandatory=False)
-    label = traits.File(argstr="-l %s", mandatory=False, exists=True,
+                                    desc=("Reclassify voxels at least some std"
+                                          " devs from the mean using some size"
+                                          " Gaussian window"))
+    label = traits.File(argstr="-l %s",  exists=True,
                         desc="Undocumented flag. Autorecon3 uses ../label/{hemisphere}.cortex.label as input file")
-    aseg = traits.File(argstr="-aseg %s", mandatory=False, exists=True,
+    aseg = traits.File(argstr="-aseg %s",  exists=True,
                        desc="Undocumented flag. Autorecon3 uses ../mri/aseg.presurf.mgz as input file")
 
 
@@ -1742,11 +1743,11 @@ class MRIsCALabelInputSpec(FSTraitedSpecOpenMP):
                     hash_files=False, name_template="%s.aparc.annot",
                     desc="Annotated surface output file")
     # optional
-    label = traits.File(argstr="-l %s", mandatory=False, exists=True,
+    label = traits.File(argstr="-l %s",  exists=True,
                         desc="Undocumented flag. Autorecon3 uses ../label/{hemisphere}.cortex.label as input file")
-    aseg = traits.File(argstr="-aseg %s", mandatory=False, exists=True,
+    aseg = traits.File(argstr="-aseg %s",  exists=True,
                        desc="Undocumented flag. Autorecon3 uses ../mri/aseg.presurf.mgz as input file")
-    seed = traits.Int(argstr="-seed %d", mandatory=False,
+    seed = traits.Int(argstr="-seed %d",
                       desc="")
     copy_inputs = traits.Bool(desc="Copies implicit inputs to node directory " +
                               "and creates a temp subjects_directory. " +
@@ -1835,8 +1836,7 @@ class SegmentCCInputSpec(FSTraitedSpec):
     subject_id = traits.String('subject_id', argstr="%s", mandatory=True,
                                position=-1, usedefault=True,
                                desc="Subject name")
-    copy_inputs = traits.Bool(mandatory=False,
-                              desc="If running as a node, set this to True." +
+    copy_inputs = traits.Bool(desc="If running as a node, set this to True." +
                               "This will copy the input files to the node " +
                               "directory.")
 
@@ -1979,10 +1979,10 @@ class EditWMwithAsegInputSpec(FSTraitedSpec):
                       desc="Input brain/T1 file")
     seg_file = File(argstr="%s", position=-2, mandatory=True, exists=True,
                     desc="Input presurf segmentation file")
-    out_file = File(argstr="%s", position=-1, mandtaory=True, exists=False,
+    out_file = File(argstr="%s", position=-1, mandatory=True, exists=False,
                     desc="File to be written as output")
     # optional
-    keep_in = traits.Bool(argstr="-keep-in", mandatory=False,
+    keep_in = traits.Bool(argstr="-keep-in",
                           desc="Keep edits as found in input volume")
 
 class EditWMwithAsegOutputSpec(TraitedSpec):

nipype/interfaces/freesurfer/registration.py

@@ -113,8 +113,8 @@ class RegisterAVItoTalairachInputSpec(FSTraitedSpec):
                   position=1, desc="The target file")
     vox2vox = File(argstr='%s', exists=True, mandatory=True,
                    position=2, desc="The vox2vox file")
-    out_file = File('talairach.auto.xfm', usedfault=True,
-                    argstr='%s', mandatory=False,
+    out_file = File('talairach.auto.xfm', usedefault=True,
+                    argstr='%s',
                     position=3, desc="The transform output")
 
 
@@ -179,10 +179,10 @@ class EMRegisterInputSpec(FSTraitedSpecOpenMP):
     skull = traits.Bool(
         argstr="-skull", desc="align to atlas containing skull (uns=5)")
     mask = File(argstr="-mask %s", exists=True,
-                mandatory=False, desc="use volume as a mask")
-    nbrspacing = traits.Int(argstr="-uns %d", mandatory=False,
+                 desc="use volume as a mask")
+    nbrspacing = traits.Int(argstr="-uns %d",
                             desc="align to atlas containing skull setting unknown_nbr_spacing = nbrspacing")
-    transform = File(argstr="-t %s", exists=True, mandatory=False,
+    transform = File(argstr="-t %s", exists=True,
                      desc="Previously computed transform")
 
 
@@ -287,9 +287,8 @@ class PaintInputSpec(FSTraitedSpec):
     template = File(argstr="%s", exists=True, mandatory=True, position=-3,
                     desc="Template file")
     # optional
-    template_param = traits.Int(
-        mandatory=False, desc="Frame number of the input template")
-    averages = traits.Int(argstr="-a %d", mandatory=False,
+    template_param = traits.Int(desc="Frame number of the input template")
+    averages = traits.Int(argstr="-a %d",
                           desc="Average curvature patterns")
     out_file = File(argstr="%s", exists=False, position=-1,
                     name_template="%s.avg_curv", hash_files=False,

nipype/interfaces/freesurfer/tests/test_auto_Aparc2Aseg.py

@@ -9,25 +9,20 @@ def test_Aparc2Aseg_inputs():
     args=dict(argstr='%s',
     ),
     aseg=dict(argstr='--aseg %s',
-    mandatory=False,
-    ),
-    copy_inputs=dict(mandatory=False,
     ),
+    copy_inputs=dict(),
     ctxseg=dict(argstr='--ctxseg %s',
-    mandatory=False,
     ),
     environ=dict(nohash=True,
     usedefault=True,
     ),
     filled=dict(),
     hypo_wm=dict(argstr='--hypo-as-wm',
-    mandatory=False,
     ),
     ignore_exception=dict(nohash=True,
     usedefault=True,
     ),
     label_wm=dict(argstr='--labelwm',
-    mandatory=False,
     ),
     lh_annotation=dict(mandatory=True,
     ),
@@ -51,7 +46,6 @@ def test_Aparc2Aseg_inputs():
     ribbon=dict(mandatory=True,
     ),
     rip_unknown=dict(argstr='--rip-unknown',
-    mandatory=False,
     ),
     subject_id=dict(argstr='--s %s',
     mandatory=True,
@@ -61,7 +55,6 @@ def test_Aparc2Aseg_inputs():
     terminal_output=dict(nohash=True,
     ),
     volmask=dict(argstr='--volmask',
-    mandatory=False,
     ),
     )
     inputs = Aparc2Aseg.input_spec()

nipype/interfaces/freesurfer/tests/test_auto_Apas2Aseg.py

@@ -31,7 +31,6 @@ def test_Apas2Aseg_inputs():
 
 def test_Apas2Aseg_outputs():
     output_map = dict(out_file=dict(argstr='%s',
-    mandatory=False,
     ),
     )
     outputs = Apas2Aseg.output_spec()

nipype/interfaces/freesurfer/tests/test_auto_CALabel.py

@@ -5,12 +5,10 @@
 
 def test_CALabel_inputs():
     input_map = dict(align=dict(argstr='-align',
-    mandatory=False,
     ),
     args=dict(argstr='%s',
     ),
     aseg=dict(argstr='-aseg %s',
-    mandatory=False,
     ),
     environ=dict(nohash=True,
     usedefault=True,
@@ -27,21 +25,17 @@ def test_CALabel_inputs():
     intensities=dict(argstr='-r %s',
     ),
     label=dict(argstr='-l %s',
-    mandatory=False,
     ),
     no_big_ventricles=dict(argstr='-nobigventricles',
-    mandatory=False,
     ),
     num_threads=dict(),
     out_file=dict(argstr='%s',
     mandatory=True,
     position=-1,
     ),
     prior=dict(argstr='-prior %.1f',
-    mandatory=False,
     ),
     relabel_unlikely=dict(argstr='-relabel_unlikely %d %.1f',
-    mandatory=False,
     ),
     subjects_dir=dict(),
     template=dict(argstr='%s',

nipype/interfaces/freesurfer/tests/test_auto_CANormalize.py

@@ -11,7 +11,6 @@ def test_CANormalize_inputs():
     position=-3,
     ),
     control_points=dict(argstr='-c %s',
-    mandatory=False,
     ),
     environ=dict(nohash=True,
     usedefault=True,
@@ -26,7 +25,6 @@ def test_CANormalize_inputs():
     long_file=dict(argstr='-long %s',
     ),
     mask=dict(argstr='-mask %s',
-    mandatory=False,
     ),
     out_file=dict(argstr='%s',
     hash_files=False,