Merge pull request #2292 from mgxd/rel/0.14.0

Rel/0.14.0

Author: mgxd

.mailmap

@@ -1,5 +1,6 @@
 Aimi Watanabe <watanabe.aimi@gmail.com> stymy <rschadmin@cmi-rsch-li002.childmind.org>
 Aimi Watanabe <watanabe.aimi@gmail.com> stymy <watanabe.aimi@gmail.com>
+Alejandro de la Vega <aleph4@gmail.com> adelavega <delavega@utexas.edu>
 Alexander Schaefer <alexschaefer83@gmail.com> Alexander Schaefer <aschaefer@melisse.cbs.mpg.de>
 Alexander Schaefer <alexschaefer83@gmail.com> alexschaefer83 <alexschaefer83@gmail.com>
 Alexander Schaefer <alexschaefer83@gmail.com> aschaefer <aschaefer@aschaefer-U36SD.(none)>
@@ -56,11 +57,13 @@ Franz Liem <franz.liem@gmail.com> fliem <franz.liem>
 Gael Varoquaux <gael.varoquaux@normalesup.org> GaelVaroquaux
 Gael Varoquaux <gael.varoquaux@normalesup.org> GaelVaroquaux <gael.varoquaux@noramlesup.org>
 Gavin Cooper <Gavin.Cooper@newcastle.edu.au> gjcooper <gjcooper@gmail.com>
+Gilles de Hollander <gilles.de.hollander@gmail.com> Gilles86 <gilles.de.hollander@gmail.com>
 Hans Johnson <hans-johnson@uiowa.edu> Hans Johnson <hans.j.johnson@gmail.com>
 Hans Johnson <hans-johnson@uiowa.edu> hjmjohnson <hans.j.johnson@gmail.com>
 Horea Christian <horea.christ@yandex.com> Horea Christian <h.chr@mail.ru>
 Isaac Schwabacher <ischwabacher@wisc.edu> ischwabacher <ischwabacher@wisc.edu>
 James Kent <james-kent@uiowa.edu> jdkent <james-kent@uiowa.edu>
+Jakub Kaczmarzyk <jakubk@mit.edu> kaczmarj <jakubk@mit.edu>
 Jason Wong <jf126dolphin@gmail.com> Jason <jf126dolphin@gmail.com>
 Jason Wong <jf126dolphin@gmail.com> jason <jf126dolphin@gmail.com>
 Jason Wong <jf126dolphin@gmail.com> Jason W <jf126dolphin@gmail.com>
@@ -72,7 +75,9 @@ Joerg Stadler <Joerg.Stadler@lin-magdeburg.de> Jörg Stadler <Stadler@lin-magdeb
 Joke Durnez <joke.durnez@gmail.com> jokedurnez <joke.durnez@gmail.com>
 Josh Warner <silvertrumpet999+github@gmail.com> Josh Warner (Mac) <warner.joshua@mayo.edu>
 Kai Schlamp <schlamp@gmx.de> medihack <schlamp@gmx.de>Jessica Forbes <jessica-forbes@uiowa.edu> jessicaforbes <jessica-forbes@uiowa.edu>
+Kevin Sitek <ksitek@mit.edu> sitek <ksitek@mit.edu>
 Leonie Lampe <leonie.lampe@gmail.com> Leonie Lmape <leonie.lampe@gmail.com>
+Lukas Snoek <lukassnoek@gmail.com> Lukas Snoek <lukassnoek@gmail.com>
 Mathias Goncalves <goncalves.mathias@gmail.com> mathiasg <mathiasg@mit.edu>
 Michael Dayan <mdayan.research@gmail.com> Michael <mdayan.research@gmail.com>
 Michael Dayan <mdayan.research@gmail.com> Michael <mdayan.comp@gmail.com>
@@ -102,5 +107,6 @@ Steven Giavasis <sgiava77@gmail.com> sgiavasis <sgiavasis@ieee.org>
 Tristan Glatard <tristan.glatard@mcgill.ca> Tristan Glatard <tristan.glatard@creatis.insa-lyon.fr>
 Victor Saase <victor@saase.net> vsaase <victor@saase.net>
 William Triplett <wtriplett@gmail.com> William Triplett <wtriplett@ufl.edu>
+Wolfgang Pauli <Wolfgang.m.Pauli@gmail.com> Wolfgang Pauli <Wolfgang.m.Pauli@gmail.com>
 Yaroslav Halchenko <debian@onerussian.com> Yaroslav Halchenko <yoh@dartmouth.edu>
 pipolose <pipolose@pipoloses-air.watson.ibm.com> pipolose <pipolose@pipoloses-MacBook-Air.local>

.travis.yml

@@ -59,4 +59,4 @@ deploy:
     tags: true
     repo: nipy/nipype
     branch: master
-  distributions: "sdist"
+  distributions: "sdist bdist_wheel"

.zenodo.json

@@ -514,11 +514,6 @@
     {
       "name": "Shachnev, Dmitry"
     },
-    {
-      "affiliation": "MIT, HMS",
-      "name": "Ghosh, Satrajit",
-      "orcid": "0000-0002-5312-6729"
-    },
     {
       "affiliation": "University of Amsterdam",
       "name": "Lukas Snoek",
@@ -538,6 +533,11 @@
       "affiliation": "MIT",
       "name": "Kaczmarzyk, Jakub",
       "orcid": "0000-0002-5544-7577"
+    },
+    {
+      "affiliation": "MIT, HMS",
+      "name": "Ghosh, Satrajit",
+      "orcid": "0000-0002-5312-6729"
     }
   ],
   "keywords": [

CHANGES

@@ -1,6 +1,14 @@
-Upcoming release (0.14.0)
+Upcoming release
 ================
 
+0.14.0 (November 21, 2017)
+==========================
+
+###### [Full changelog](https://github.com/nipy/nipype/milestone/13)
+
+* ENH: Generate Dockerfiles with neurodocker (https://github.com/nipy/nipype/pull/2202)
+* ENH: FLAIR options for recon-all (https://github.com/nipy/nipype/pull/2279)
+* ENH: Config option for setting maxtasksperchild when multiprocessing (https://github.com/nipy/nipype/pull/2284)
 * FIX: Testing maintainance and improvements (https://github.com/nipy/nipype/pull/2252)
 * ENH: Add elapsed_time and final metric_value to ants.Registration (https://github.com/nipy/nipype/pull/1985)
 * ENH: Improve terminal_output feature (https://github.com/nipy/nipype/pull/2209)
@@ -17,7 +25,7 @@ Upcoming release (0.14.0)
 * MAINT: Additional Windows support (https://github.com/nipy/nipype/pull/2085)
 * ENH: Output realignment matrices from TOPUP (https://github.com/nipy/nipype/pull/2084)
 * ENH: Additional AFNI interfaces: 3dZcat, 3dZeropad, 3dedge3, 3dDeconvolve, 3dQwarp, 1dCat, 3dNwarpApply, 3daxialize,
-       3dREMLfit, 3dUndump, 3dCM, 3dSynthesize + more (https://github.com/nipy/nipype/pull/2087, https://github.com/nipy/nipype/pull/2090, 
+       3dREMLfit, 3dUndump, 3dCM, 3dSynthesize + more (https://github.com/nipy/nipype/pull/2087, https://github.com/nipy/nipype/pull/2090,
        https://github.com/nipy/nipype/pull/2095, https://github.com/nipy/nipype/pull/2099, https://github.com/nipy/nipype/pull/2103,
        https://github.com/nipy/nipype/pull/2114, https://github.com/nipy/nipype/pull/2135, https://github.com/nipy/nipype/pull/2186,
        https://github.com/nipy/nipype/pull/2201, https://github.com/nipy/nipype/pull/2210)

doc/conf.py

@@ -82,7 +82,7 @@
 # The short X.Y version.
 version = nipype.__version__
 # The full version, including alpha/beta/rc tags.
-release = "0.13.1"
+release = "0.14.0-rc1"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/users/config_file.rst

@@ -74,11 +74,11 @@ Execution
 
 *display_variable*
 	Override the ``$DISPLAY`` environment variable for interfaces that require
-    an X server. This option is useful if there is a running X server, but 
-    ``$DISPLAY`` was not defined in nipype's environment. For example, if an X 
+    an X server. This option is useful if there is a running X server, but
+    ``$DISPLAY`` was not defined in nipype's environment. For example, if an X
     server is listening on the default port of 6000, set ``display_variable = :0``
-    to enable nipype interfaces to use it. It may also point to displays provided 
-    by VNC, `xnest <http://www.x.org/archive/X11R7.5/doc/man/man1/Xnest.1.html>`_ 
+    to enable nipype interfaces to use it. It may also point to displays provided
+    by VNC, `xnest <http://www.x.org/archive/X11R7.5/doc/man/man1/Xnest.1.html>`_
     or `Xvfb <http://www.x.org/archive/X11R6.8.1/doc/Xvfb.1.html>`_.
     If neither ``display_variable`` nor the ``$DISPLAY`` environment variable are
     set, nipype will try to configure a new virtual server using Xvfb.

nipype/algorithms/tests/test_mesh_ops.py

@@ -15,7 +15,7 @@
 
 @pytest.mark.skipif(VTKInfo.no_tvtk(), reason="tvtk is not installed")
 def test_ident_distances(tmpdir):
-    tmpdir.chdir() 
+    tmpdir.chdir()
 
     in_surf = example_data('surf01.vtk')
     dist_ident = m.ComputeMeshWarp()

nipype/info.py

@@ -10,7 +10,7 @@
 # full release.  '.dev' as a version_extra string means this is a development
 # version
 # Remove -dev for release
-__version__ = '1.0.0-dev'
+__version__ = '0.14.0-rc1'
 
 
 def get_nipype_gitversion():

nipype/interfaces/afni/tests/test_auto_TCatSubBrick.py

@@ -0,0 +1,48 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..utils import TCatSubBrick
+
+
+def test_TCatSubBrick_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_files=dict(argstr='%s%s ...',
+    copyfile=False,
+    mandatory=True,
+    position=-1,
+    ),
+    num_threads=dict(nohash=True,
+    usedefault=True,
+    ),
+    out_file=dict(argstr='-prefix %s',
+    genfile=True,
+    ),
+    outputtype=dict(),
+    rlt=dict(argstr='-rlt%s',
+    position=1,
+    ),
+    terminal_output=dict(deprecated='1.0.0',
+    nohash=True,
+    ),
+    )
+    inputs = TCatSubBrick.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_TCatSubBrick_outputs():
+    output_map = dict(out_file=dict(),
+    )
+    outputs = TCatSubBrick.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/ants/tests/test_resampling.py

@@ -1,5 +1,5 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
-# vi: set ft=python sts=4 ts=4 sw=4 et:                                                                                                                 
+# vi: set ft=python sts=4 ts=4 sw=4 et:
 
 from nipype.interfaces.ants import WarpImageMultiTransform, WarpTimeSeriesImageMultiTransform
 import os
@@ -66,7 +66,7 @@ def create_wtsimt():
 def test_WarpTimeSeriesImageMultiTransform(change_dir, create_wtsimt):
    wtsimt = create_wtsimt
    assert wtsimt.cmdline == 'WarpTimeSeriesImageMultiTransform 4 resting.nii resting_wtsimt.nii \
--R ants_deformed.nii.gz ants_Warp.nii.gz ants_Affine.txt'                                                                                            
+-R ants_deformed.nii.gz ants_Warp.nii.gz ants_Affine.txt'
 
 
 def test_WarpTimeSeriesImageMultiTransform_invaffine(change_dir, create_wtsimt):

nipype/interfaces/cmtk/tests/test_nbs.py

@@ -31,12 +31,12 @@ def test_importerror(creating_graphs, tmpdir):
     graphlist = creating_graphs
     group1 = graphlist[:3]
     group2 = graphlist[3:]
-    
+
     nbs = NetworkBasedStatistic()
     nbs.inputs.in_group1 = group1
     nbs.inputs.in_group2 = group2
     nbs.inputs.edge_key = "weight"
-    
+
     with pytest.raises(ImportError) as e:
         nbs.run()
     assert "cviewer library is not available" == str(e.value)

nipype/interfaces/niftyfit/asl.py

@@ -147,7 +147,7 @@ class FitAsl(NiftyFitCommand):
     >>> from nipype.interfaces import niftyfit
     >>> node = niftyfit.FitAsl()
     >>> node.inputs.source_file = 'asl.nii.gz'
-    >>> node.cmdline  
+    >>> node.cmdline
     'fit_asl -source asl.nii.gz -cbf asl_cbf.nii.gz -error asl_error.nii.gz \
 -syn asl_syn.nii.gz'
 

nipype/interfaces/tests/test_auto_SimpleInterface.py

@@ -0,0 +1,16 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..base import SimpleInterface
+
+
+def test_SimpleInterface_inputs():
+    input_map = dict(ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    )
+    inputs = SimpleInterface.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value
+

nipype/pipeline/engine/tests/test_utils.py

@@ -23,7 +23,7 @@ def test_identitynode_removal(tmpdir):
     def test_function(arg1, arg2, arg3):
         import numpy as np
         return (np.array(arg1) + arg2 + arg3).tolist()
-    
+
 
     wf = pe.Workflow(name="testidentity", base_dir=tmpdir.strpath)
 

setup.cfg

@@ -0,0 +1,2 @@
+[bdist_wheel]
+universal=1