Merge branch 'master' into enh/MRTrix3

Conflicts:
	CHANGES

Author: oesteban

.gitignore

@@ -14,4 +14,6 @@
 .pydevproject
 .idea/
 /documentation.zip
-.DS_Store
+.DS_Store
+nipype/testing/data/von-ray_errmap.nii.gz
+nipype/testing/data/von_errmap.nii.gz

.mailmap

@@ -4,7 +4,7 @@ Cindee Madison <[email protected]> cindeem
 Chris Filo Gorgolewski <[email protected]> filo <filo@filo-Precision-M6500>
 Chris Filo Gorgolewski <[email protected]> Krzysztof Gorgolewski <[email protected]>
 Erik Ziegler <[email protected]> erikz <[email protected]>
-Michael Waskom <[email protected]> mwaskom <[email protected]> Michael Waskom <[email protected]> mwaskom <[email protected]> 
+Michael Waskom <[email protected]> mwaskom <[email protected]> Michael Waskom <[email protected]> mwaskom <[email protected]>
 Gael Varoquaux <[email protected]> GaelVaroquaux
 Gael Varoquaux <[email protected]> GaelVaroquaux <[email protected]>
 Daniel Ginsburg <[email protected]> danginsburg <[email protected]>

.travis.yml

@@ -45,4 +45,5 @@ deploy:
     secure: ZaN6Y4hfybPMi1rW3Qe03irCe/3GU4J4BJsjG+tClVN5Fjc3FCJaYU0k4wNd9q2kMjuRDv1efA9BN/5QasJS32oqs6wHvxzIWA18ucel4BBnAAkuviC1vqi/8Hk/DGB6e1gnmZ1Nv58zVLfn0MwlOKmsGDtvGQWc+HbaV2fS5NA=
   on:
     tags: true
+    repo: nipy/nipype
     branch: master

CHANGES

@@ -2,6 +2,10 @@ Next release
 ============
 
 * ENH: New interfaces for MRTrix3 (https://github.com/nipy/nipype/pull/1126)
+* ENH: New option in afni.3dRefit - zdel, ydel, zdel etc. (https://github.com/nipy/nipype/pull/1079)
+* FIX: ants.Registration composite transform outputs are no longer returned as lists (https://github.com/nipy/nipype/pull/1183)
+* BUG: ANTs Registration interface failed with multi-modal inputs
+    (https://github.com/nipy/nipype/pull/1176) (https://github.com/nipy/nipype/issues/1175)
 * FIX: Bug in XFibres5 (https://github.com/nipy/nipype/pull/1168)
 * ENH: Attempt to use hard links for data sink.
     (https://github.com/nipy/nipype/pull/1161)

Makefile

@@ -5,6 +5,8 @@
 PYTHON ?= python
 NOSETESTS ?= nosetests
 
+.PHONY: zipdoc sdist egg upload_to_pypi trailing-spaces clean-pyc clean-so clean-build clean-ctags clean in inplace test-code test-doc test-coverage test html specs check-before-commit check
+
 zipdoc: html
 	zip documentation.zip doc/_build/html
 
@@ -26,7 +28,7 @@ upload_to_pypi: zipdoc
 	python setup.py sdist --formats=zip,gztar upload
 
 trailing-spaces:
-	find . -name "*.py" | xargs perl -pi -e 's/[ \t]*$$//'
+	find . -name "*[.py|.rst]" -type f | xargs perl -pi -e 's/[ \t]*$$//'
 	@echo "Reverting test_docparse"
 	git checkout nipype/utils/tests/test_docparse.py
 
@@ -70,6 +72,7 @@ specs:
 	@echo "Checking specs and autogenerating spec tests"
 	python tools/checkspecs.py
 
+check: check-before-commit # just a shortcut
 check-before-commit: specs trailing-spaces html test
 	@echo "removed spaces"
 	@echo "built docs"

README.rst

@@ -4,13 +4,13 @@ NIPYPE: Neuroimaging in Python: Pipelines and Interfaces
 
 .. image:: https://travis-ci.org/nipy/nipype.png?branch=master
   :target: https://travis-ci.org/nipy/nipype
-  
+
 .. image:: https://circleci.com/gh/nipy/nipype/tree/master.svg?style=svg
   :target: https://circleci.com/gh/nipy/nipype/tree/master
 
 .. image:: https://coveralls.io/repos/nipy/nipype/badge.png
   :target: https://coveralls.io/r/nipy/nipype
-  
+
 .. image:: https://www.codacy.com/project/badge/182f27944c51474490b369d0a23e2f32
   :target: https://www.codacy.com/app/krzysztof-gorgolewski/nipy_nipype
 
@@ -70,7 +70,7 @@ Website
 -------
 
 Information specific to Nipype is located here::
-	    
+
     http://nipy.org/nipype
 
 
@@ -81,10 +81,10 @@ If you have a problem or would like to ask a question about how to do something
 to `NeuroStars.org <http://neurostars.org>`_ with a *nipype* tag. `NeuroStars.org <http://neurostars.org>`_  is a platform similar to StackOverflow but dedicated to neuroinformatics. All previous Nipype questions are available here::
 
        http://neurostars.org/t/nipype/
-	   
+
 
 To participate in the Nipype development related discussions please use the following mailing list::
-       
+
        http://mail.python.org/mailman/listinfo/neuroimaging
 
 Please add *[nipype]* to the subject line when posting on the mailing list.
@@ -96,7 +96,7 @@ Nipype structure
 Currently Nipype consists of the following files and directories:
 
   INSTALL
-    NIPYPE prerequisites, installation, development, testing, and 
+    NIPYPE prerequisites, installation, development, testing, and
     troubleshooting.
 
   README

THANKS.rst

@@ -86,15 +86,15 @@ Other contributors
   * Mike Trumpis
   * Karl Young
   * Tom Waite
-  
+
 We would also like to thank `JetBrains <http://www.jetbrains.com/>`__ for providing `Pycharm <http://www.jetbrains.com/pycharm/>`__ licenses.
- 
+
 Funding
 -------
 Satrajit Ghosh work on this project was partially funded by NIBIB R03 EB008673 (PI: Ghosh and Whitfield-Gabrieli) and by the `INCF <http://www.incf.org>`__ through a contract with TankThink Labs, LLC.
-Chris Burns was supported by NIMH grant 5R01MH081909-02 (PI: Desposito). Hans Jonson was supported by 
-`2 U54 EB005149 - 06	 Core 2b Huntington's Disease - Driving Biological Project <http://projectreporter.nih.gov/project_info_description.cfm?aid=8153616&icde=16158743&ddparam=&ddvalue=&ddsub=&cr=18&csb=PT&cs=ASC>`__, 
-`S10 RR023392	 Enterprise Storage In A Collaborative Neuroimaging Environment	 <http://projectreporter.nih.gov/project_info_description.cfm?aid=7209718&icde=16158552&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC>`__, 
-`R01 NS040068	 Neurobiological Predictors of Huntington's Disease	 <http://projectreporter.nih.gov/project_info_description.cfm?aid=6266377&icde=16158103>`__, 
+Chris Burns was supported by NIMH grant 5R01MH081909-02 (PI: Desposito). Hans Jonson was supported by
+`2 U54 EB005149 - 06	 Core 2b Huntington's Disease - Driving Biological Project <http://projectreporter.nih.gov/project_info_description.cfm?aid=8153616&icde=16158743&ddparam=&ddvalue=&ddsub=&cr=18&csb=PT&cs=ASC>`__,
+`S10 RR023392	 Enterprise Storage In A Collaborative Neuroimaging Environment	 <http://projectreporter.nih.gov/project_info_description.cfm?aid=7209718&icde=16158552&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC>`__,
+`R01 NS040068	 Neurobiological Predictors of Huntington's Disease	 <http://projectreporter.nih.gov/project_info_description.cfm?aid=6266377&icde=16158103>`__,
 and `UL1 TR000442	University of Iowa Clinical and Translational Science Program <http://projectreporter.nih.gov/project_info_description.cfm?aid=8467220&icde=16159156&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC>`__.
 

doc/README.txt

@@ -16,7 +16,7 @@ Discover available make targets::
   make help
 
 Clean up previous build::
-  
+
   make clean
 
 Build html documentation::

doc/_templates/sidebar_versions.html

@@ -17,7 +17,7 @@ <h3>{{ _('Versions') }}</h3>
                 <td align="left">Release</td><td align="right">Devel</td>
             </tr>
             <tr>
-                <td align="left">0.10.0</td><td align="right">{{ version }}</td>
+                <td align="left">0.11.0-rc1</td><td align="right">{{ version }}</td>
             </tr>
             <tr>
                 <td align="left"><a href="{{pathto('users/install')}}">Download</a></td>

doc/devel/gitwash/configure_git.rst

@@ -16,15 +16,15 @@ Here is an example ``.gitconfig`` file::
   [user]
           name = Your Name
           email = [email protected]
-  
+
   [alias]
           ci = commit -a
           co = checkout
           st = status -a
           stat = status -a
           br = branch
           wdiff = diff --color-words
-  
+
   [core]
           editor = vim
 
@@ -33,7 +33,7 @@ Here is an example ``.gitconfig`` file::
 
 You can edit this file directly or you can use the ``git config --global``
 command::
-  
+
   git config --global user.name "Your Name"
   git config --global user.email [email protected]
   git config --global alias.ci "commit -a"