Merge pull request #2292 from mgxd/rel/0.14.0

Rel/0.14.0

Author: mgxd

.mailmap

@@ -1,5 +1,6 @@
 Aimi Watanabe <[email protected]> stymy <[email protected]>
 Aimi Watanabe <[email protected]> stymy <[email protected]>
+Alejandro de la Vega <[email protected]> adelavega <[email protected]>
 Alexander Schaefer <[email protected]> Alexander Schaefer <[email protected]>
 Alexander Schaefer <[email protected]> alexschaefer83 <[email protected]>
 Alexander Schaefer <[email protected]> aschaefer <aschaefer@aschaefer-U36SD.(none)>
@@ -56,11 +57,13 @@ Franz Liem <[email protected]> fliem <franz.liem>
 Gael Varoquaux <[email protected]> GaelVaroquaux
 Gael Varoquaux <[email protected]> GaelVaroquaux <[email protected]>
 Gavin Cooper <[email protected]> gjcooper <[email protected]>
+Gilles de Hollander <[email protected]> Gilles86 <[email protected]>
 Hans Johnson <[email protected]> Hans Johnson <[email protected]>
 Hans Johnson <[email protected]> hjmjohnson <[email protected]>
 Horea Christian <[email protected]> Horea Christian <[email protected]>
 Isaac Schwabacher <[email protected]> ischwabacher <[email protected]>
 James Kent <[email protected]> jdkent <[email protected]>
+Jakub Kaczmarzyk <[email protected]> kaczmarj <[email protected]>
 Jason Wong <[email protected]> Jason <[email protected]>
 Jason Wong <[email protected]> jason <[email protected]>
 Jason Wong <[email protected]> Jason W <[email protected]>
@@ -72,7 +75,9 @@ Joerg Stadler <[email protected]> Jörg Stadler <Stadler@lin-magdeb
 Joke Durnez <[email protected]> jokedurnez <[email protected]>
 Josh Warner <[email protected]> Josh Warner (Mac) <[email protected]>
 Kai Schlamp <[email protected]> medihack <[email protected]>Jessica Forbes <[email protected]> jessicaforbes <[email protected]>
+Kevin Sitek <[email protected]> sitek <[email protected]>
 Leonie Lampe <[email protected]> Leonie Lmape <[email protected]>
+Lukas Snoek <[email protected]> Lukas Snoek <[email protected]>
 Mathias Goncalves <[email protected]> mathiasg <[email protected]>
 Michael Dayan <[email protected]> Michael <[email protected]>
 Michael Dayan <[email protected]> Michael <[email protected]>
@@ -102,5 +107,6 @@ Steven Giavasis <[email protected]> sgiavasis <[email protected]>
 Tristan Glatard <[email protected]> Tristan Glatard <[email protected]>
 Victor Saase <[email protected]> vsaase <[email protected]>
 William Triplett <[email protected]> William Triplett <[email protected]>
+Wolfgang Pauli <[email protected]> Wolfgang Pauli <[email protected]>
 Yaroslav Halchenko <[email protected]> Yaroslav Halchenko <[email protected]>
 pipolose <[email protected]> pipolose <[email protected]>

.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):