Merge remote-tracking branch 'upstream/master' into fix/frompy3

* upstream/master:
  STYLE: Autogenerated files ignored
  ENH: More end-of-line whitespace removed.
  ENH: Improve the removal of trailing whitespace
  updted changelog
  remove tests
  added info about composite transforms
  BUG: Restore registration interface failed multi-modal
  STYLE: Remove end of line trailing white space
  fixed doctests
  fixed syntax
  there is always only one composite transform - a list is not appropriate here
  Current ANTS doctests are only valid for unimodal registrations
  Revert "BUG: Registration interface failed multi-modal"
  better handling of errors when using caching
  out dir for epi_reg is compulsory but meaningless for nipype
  added circleCI and codacy badges
  fixed dir making
  adding tests
  adding further options to 3drefit

Author: satra

.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 <cindee@berkeley.edu> cindeem
 Chris Filo Gorgolewski <chris.gorgolewski@gmail.com> filo <filo@filo-Precision-M6500>
 Chris Filo Gorgolewski <chris.gorgolewski@gmail.com> Krzysztof Gorgolewski <krzysztof.gorgolewski@gmail.com>
 Erik Ziegler <erik.ziegler@ulg.ac.be> erikz <erik.ziegler@ulg.ac.be>
-Michael Waskom <mwaskom@stanford.edu> mwaskom <mwaskom@stanford.edu> Michael Waskom <mwaskom@mit.edu> mwaskom <mwaskom@mit.edu> 
+Michael Waskom <mwaskom@stanford.edu> mwaskom <mwaskom@stanford.edu> Michael Waskom <mwaskom@mit.edu> mwaskom <mwaskom@mit.edu>
 Gael Varoquaux <gael.varoquaux@normalesup.org> GaelVaroquaux
 Gael Varoquaux <gael.varoquaux@normalesup.org> GaelVaroquaux <gael.varoquaux@noramlesup.org>
 Daniel Ginsburg <daniel.ginsburg@childrens.harvard.edu> danginsburg <daniel.ginsburg@childrens.harvard.edu>

CHANGES

@@ -1,6 +1,8 @@
 Next release
 ============
 
+* 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)

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

@@ -5,9 +5,15 @@ 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
+
 .. image:: https://img.shields.io/pypi/v/nipype.svg
     :target: https://pypi.python.org/pypi/nipype/
     :alt: Latest Version
@@ -64,7 +70,7 @@ Website
 -------
 
 Information specific to Nipype is located here::
-	    
+
     http://nipy.org/nipype
 
 
@@ -75,10 +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.
@@ -90,7 +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>`__.
 

circle.yml

@@ -18,7 +18,7 @@ dependencies:
     - sudo apt-key adv --recv-keys --keyserver hkp://pgp.mit.edu:80 0xA5D32F012649A5A9
     - sudo apt-get update -y; sudo apt-get install -y fsl-core fsl-atlases
     - bash ~/nipype/tools/install_spm_mcr.sh
-    - mkdir ~/.nipype && echo "[logging]" > ~/.nipype/nipype.cfg && echo "workflow_level = DEBUG" >> ~/.nipype/nipype.cfg && echo "interface_level = DEBUG" >> ~/.nipype/nipype.cfg && echo "filemanip_level = DEBUG" >> ~/.nipype/nipype.cfg
+    - mkdir -p ~/.nipype && echo "[logging]" > ~/.nipype/nipype.cfg && echo "workflow_level = DEBUG" >> ~/.nipype/nipype.cfg && echo "interface_level = DEBUG" >> ~/.nipype/nipype.cfg && echo "filemanip_level = DEBUG" >> ~/.nipype/nipype.cfg
 test:
   override:
     - . /usr/share/fsl/5.0/etc/fslconf/fsl.sh && nosetests --with-doctest --logging-level=DEBUG --verbosity=3:

doc/README.txt

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

doc/devel/gitwash/configure_git.rst

@@ -16,15 +16,15 @@ Here is an example ``.gitconfig`` file::
   [user]
           name = Your Name
           email = you@yourdomain.example.com
-  
+
   [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 you@yourdomain.example.com
   git config --global alias.ci "commit -a"

doc/devel/gitwash/development_workflow.rst

@@ -22,7 +22,7 @@ Workflow summary
 This way of working really helps to keep work well organized, and in
 keeping history as clear as possible.
 
-See |emdash| for example |emdash| `linux git workflow`_. 
+See |emdash| for example |emdash| `linux git workflow`_.
 
 Making a new feature branch
 ===========================
@@ -44,7 +44,7 @@ In git >1.7 you can ensure that the link is correctly set by using the
 ``--set-upstream`` option::
 
    git push --set-upstream origin my-new-feature
-   
+
 From now on git_ will know that ``my-new-feature`` is related to the
 ``my-new-feature`` branch in the github_ repo.
 
@@ -83,7 +83,7 @@ In more detail
 
 #. Check what the actual changes are with ``git diff`` (`git diff`_).
 #. Add any new files to version control ``git add new_file_name`` (see
-   `git add`_). 
+   `git add`_).
 #. To commit all modified files into the local copy of your repo,, do
    ``git commit -am 'A commit message'``.  Note the ``-am`` options to
    ``commit``. The ``m`` flag just signals that you're going to type a
@@ -92,7 +92,7 @@ In more detail
    description in the `tangled working copy problem`_. The `git commit`_ manual
    page might also be useful.
 #. To push the changes up to your forked repo on github_, do a ``git
-   push`` (see `git push`). 
+   push`` (see `git push`).
 
 Asking for code review
 ======================
@@ -121,7 +121,7 @@ Asking for code review
 The generated comparison, is between your feature branch
 ``my-new-feature``, and the place in ``master`` from which you branched
 ``my-new-feature``.  In other words, you can keep updating ``master``
-without interfering with the output from the comparison.  More detail? 
+without interfering with the output from the comparison.  More detail?
 Note the three dots in the URL above (``master...my-new-feature``).
 
 .. admonition:: Two vs three dots
@@ -165,7 +165,7 @@ When you are ready to ask for the merge of your code:
 Merging from trunk
 ==================
 
-This updates your code from the upstream `nipype github`_  repo. 
+This updates your code from the upstream `nipype github`_  repo.
 
 Overview
 --------

doc/devel/gitwash/git_development.rst

@@ -13,4 +13,4 @@ Contents:
    set_up_fork
    configure_git
    development_workflow
-   
+

doc/devel/gitwash/git_resources.rst

@@ -9,9 +9,9 @@ Tutorials and summaries
 
 * `github help`_ has an excellent series of how-to guides.
 * `learn.github`_ has an excellent series of tutorials
-* The `pro git book`_ is a good in-depth book on git. 
+* The `pro git book`_ is a good in-depth book on git.
 * A `git cheat sheet`_ is a page giving summaries of common commands.
-* The `git user manual`_ 
+* The `git user manual`_
 * The `git tutorial`_
 * The `git community book`_
 * `git ready`_ |emdash| a nice series of tutorials

doc/devel/gitwash/set_up_fork.rst

@@ -4,7 +4,7 @@
  Set up your fork
 ==================
 
-First you follow the instructions for :ref:`forking`. 
+First you follow the instructions for :ref:`forking`.
 
 Overview
 ========

doc/devel/index.rst

@@ -15,7 +15,7 @@ conventions documented in the `NIPY Developers Guide
    :maxdepth: 2
 
    writing_custom_interfaces
-   gitwash/index   
+   gitwash/index
    architecture
    provenance
    software_using_nipype