Merge remote-tracking branch 'nipy/master'

Author: tsalo

CHANGES

@@ -1,6 +1,7 @@
 Upcoming Release
 =====================
 
+* ENH: Sphinx extension to plot workflows (https://github.com/nipy/nipype/pull/1896)
 * ENH: Added non-steady state detector for EPI data (https://github.com/nipy/nipype/pull/1839)
 * ENH: Enable new BBRegister init options for FSv6+ (https://github.com/nipy/nipype/pull/1811)
 * REF: Splits nipype.interfaces.utility into base, csv, and wrappers (https://github.com/nipy/nipype/pull/1828)
@@ -22,7 +23,7 @@ Upcoming Release
 
 0.13.0-rc1 (January 4, 2017)
 ===============================
- 
+
 * FIX: Compatibility with traits 4.6 (https://github.com/nipy/nipype/pull/1770)
 * FIX: Multiproc deadlock (https://github.com/nipy/nipype/pull/1756)
 * TST: Replace nose and unittest with pytest (https://github.com/nipy/nipype/pull/1722, https://github.com/nipy/nipype/pull/1751)

doc/conf.py

@@ -42,16 +42,16 @@
 # Add any Sphinx extension module names here, as strings. They can be extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
 extensions = ['sphinx.ext.todo',
-              'sphinx.ext.pngmath',
+              'sphinx.ext.imgmath',
               'sphinx.ext.inheritance_diagram',
               'sphinx.ext.graphviz',
               'sphinx.ext.autodoc',
               'sphinx.ext.doctest',
-              'sphinx.ext.pngmath',
               'sphinx.ext.autosummary',
               'numpy_ext.numpydoc',
               'matplotlib.sphinxext.plot_directive',
               'matplotlib.sphinxext.only_directives',
+              'nipype.sphinxext.plot_workflow',
               #'IPython.sphinxext.ipython_directive',
               #'IPython.sphinxext.ipython_console_highlighting'
               ]

doc/documentation.rst

@@ -24,10 +24,12 @@ Previous versions:  `0.12.0 <http://nipype.readthedocs.io/en/0.12.0/>`_ `0.11.0
             :maxdepth: 2
 
             users/index
+            
          .. toctree::
             :maxdepth: 1
 
             changes
+
        * Developer
 
          .. toctree::

doc/users/index.rst

@@ -39,6 +39,8 @@
    mipav
    nipypecmd
    aws
+   resource_sched_profiler
+   sphinx_ext
 
 
 

doc/users/sphinx_ext.rst

@@ -0,0 +1,14 @@
+
+.. _sphinx_ext:
+
+Sphinx extensions
+-----------------
+
+
+To help users document their *Nipype*-based code, the software is shipped
+with a set of extensions (currently only one) to customize the appearance
+and simplify the generation process.
+
+.. automodule:: nipype.sphinxext.plot_workflow
+    :undoc-members:
+    :noindex:

nipype/info.py

@@ -152,7 +152,7 @@ def get_nipype_gitversion():
 ]
 
 EXTRA_REQUIRES = {
-    'doc': ['Sphinx>=0.3', 'matplotlib', 'pydotplus'],
+    'doc': ['Sphinx>=1.4', 'matplotlib', 'pydotplus'],
     'tests': TESTS_REQUIRES,
     'fmri': ['nitime', 'nilearn', 'dipy', 'nipy', 'matplotlib'],
     'profiler': ['psutil'],

nipype/interfaces/afni/utils.py

@@ -115,7 +115,8 @@ class AutoboxInputSpec(AFNICommandInputSpec):
         desc='Number of extra voxels to pad on each side of box')
     out_file = File(
         argstr='-prefix %s',
-        name_source='in_file')
+        name_source='in_file',
+        name_template='%s_autobox')
     no_clustering = traits.Bool(
         argstr='-noclust',
         desc='Don\'t do any clustering to find box. Any non-zero voxel will '
@@ -151,7 +152,7 @@ class Autobox(AFNICommand):
     >>> abox.inputs.in_file = 'structural.nii'
     >>> abox.inputs.padding = 5
     >>> abox.cmdline  # doctest: +ALLOW_UNICODE
-    '3dAutobox -input structural.nii -prefix structural_generated -npad 5'
+    '3dAutobox -input structural.nii -prefix structural_autobox -npad 5'
     >>> res = abox.run()  # doctest: +SKIP
 
     """
@@ -161,7 +162,7 @@ class Autobox(AFNICommand):
     output_spec = AutoboxOutputSpec
 
     def aggregate_outputs(self, runtime=None, needed_outputs=None):
-        outputs = self._outputs()
+        outputs = super(Autobox, self).aggregate_outputs(runtime, needed_outputs)
         pattern = 'x=(?P<x_min>-?\d+)\.\.(?P<x_max>-?\d+)  '\
                   'y=(?P<y_min>-?\d+)\.\.(?P<y_max>-?\d+)  '\
                   'z=(?P<z_min>-?\d+)\.\.(?P<z_max>-?\d+)'
@@ -172,13 +173,8 @@ def aggregate_outputs(self, runtime=None, needed_outputs=None):
                 for k in list(d.keys()):
                     d[k] = int(d[k])
                 outputs.set(**d)
-        outputs.set(out_file=self._gen_filename('out_file'))
         return outputs
 
-    def _gen_filename(self, name):
-        if name == 'out_file' and (not isdefined(self.inputs.out_file)):
-            return Undefined
-        return super(Autobox, self)._gen_filename(name)
 
 
 class BrickStatInputSpec(CommandLineInputSpec):

nipype/interfaces/freesurfer/__init__.py

@@ -21,7 +21,7 @@
                     MRIFill, MRIsInflate, Sphere, FixTopology, EulerNumber,
                     RemoveIntersection, MakeSurfaces, Curvature, CurvatureStats,
                     Jacobian, MRIsCalc, VolumeMask, ParcellationStats, Contrast,
-                    RelabelHypointensities, Aparc2Aseg, Apas2Aseg)
+                    RelabelHypointensities, Aparc2Aseg, Apas2Aseg, MRIsExpand)
 from .longitudinal import (RobustTemplate, FuseSegmentations)
 from .registration import (MPRtoMNI305, RegisterAVItoTalairach, EMRegister, Register,
                            Paint)

nipype/interfaces/freesurfer/tests/test_auto_MRIsExpand.py

@@ -0,0 +1,69 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..utils import MRIsExpand
+
+
+def test_MRIsExpand_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    distance=dict(argstr='%g',
+    mandatory=True,
+    position=-2,
+    ),
+    dt=dict(argstr='-T %g',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_file=dict(argstr='%s',
+    copyfile=False,
+    mandatory=True,
+    position=-3,
+    ),
+    navgs=dict(argstr='-navgs %d %d',
+    ),
+    nsurfaces=dict(argstr='-N %d',
+    ),
+    out_name=dict(argstr='%s',
+    position=-1,
+    usedefault=True,
+    ),
+    pial=dict(argstr='-pial %s',
+    copyfile=False,
+    ),
+    smooth_averages=dict(argstr='-A %d',
+    ),
+    sphere=dict(copyfile=False,
+    usedefault=True,
+    ),
+    spring=dict(argstr='-S %g',
+    ),
+    subjects_dir=dict(),
+    terminal_output=dict(nohash=True,
+    ),
+    thickness=dict(argstr='-thickness',
+    ),
+    thickness_name=dict(argstr='-thickness_name %s',
+    copyfile=False,
+    ),
+    write_iterations=dict(argstr='-W %d',
+    ),
+    )
+    inputs = MRIsExpand.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value
+
+
+def test_MRIsExpand_outputs():
+    output_map = dict(out_file=dict(),
+    )
+    outputs = MRIsExpand.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.traits()[key], metakey) == value

nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py

@@ -124,17 +124,25 @@ def test_ReconAll_outputs():
     aparc_stats=dict(altkey='aparc',
     loc='stats',
     ),
+    area_pial=dict(altkey='area.pial',
+    loc='surf',
+    ),
     aseg=dict(loc='mri',
     ),
     aseg_stats=dict(altkey='aseg',
     loc='stats',
     ),
+    avg_curv=dict(loc='surf',
+    ),
     brain=dict(loc='mri',
     ),
     brainmask=dict(loc='mri',
     ),
     curv=dict(loc='surf',
     ),
+    curv_pial=dict(altkey='curv.pial',
+    loc='surf',
+    ),
     curv_stats=dict(altkey='curv',
     loc='stats',
     ),
@@ -145,6 +153,8 @@ def test_ReconAll_outputs():
     ),
     inflated=dict(loc='surf',
     ),
+    jacobian_white=dict(loc='surf',
+    ),
     label=dict(altkey='*label',
     loc='label',
     ),