fix: resolved conflict

Author: satra

.gitignore

@@ -5,6 +5,7 @@
 /nipype/build
 /nipype/nipype.egg-info
 /doc/_build
+/doc/preproc
 /doc/users/examples
 /doc/api/generated
 *.pyc
@@ -14,3 +15,13 @@
 .pydevproject
 .idea/
 /documentation.zip
+.DS_Store
+nipype/testing/data/von-ray_errmap.nii.gz
+nipype/testing/data/von_errmap.nii.gz
+crash*.pklz
+.coverage
+htmlcov/
+__pycache__/
+*~
+.ipynb_checkpoints/
+.ruby-version

.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>

.noserc

@@ -0,0 +1,11 @@
+[nosetests]
+verbosity=3
+
+with-coverage=1
+cover-branches=1
+cover-xml=1
+cover-xml-file=./coverage.xml
+cover-min-percentage=50
+
+
+with-xunit=1

.travis.yml

@@ -1,42 +1,72 @@
 cache:
-  - apt
+- apt
 language: python
 python:
-  - 2.7
+- 2.7
+- 3.4
+- 3.5
 env:
-  - INSTALL_DEB_DEPENDECIES=true
-  - INSTALL_DEB_DEPENDECIES=false
-# Setup anaconda
+- INSTALL_DEB_DEPENDECIES=true
+- INSTALL_DEB_DEPENDECIES=false
 before_install:
-  - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh; else wget http://repo.continuum.io/miniconda/Miniconda3-3.6.0-Linux-x86_64.sh -O miniconda.sh; fi
-  - chmod +x miniconda.sh
-  - ./miniconda.sh -b
-  - export PATH=/home/travis/miniconda/bin:$PATH
-  - if $INSTALL_DEB_DEPENDECIES; then sudo rm -rf /dev/shm; fi
-  - if $INSTALL_DEB_DEPENDECIES; then sudo ln -s /run/shm /dev/shm; fi
-  - if $INSTALL_DEB_DEPENDECIES; then bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh); fi
-  - if $INSTALL_DEB_DEPENDECIES; then travis_retry sudo apt-get install -qq --no-install-recommends fsl afni elastix; fi
-  - if $INSTALL_DEB_DEPENDECIES; then travis_retry sudo apt-get install -qq fsl-atlases; fi
-  - if $INSTALL_DEB_DEPENDECIES; then source /etc/fsl/fsl.sh; fi
-
-# Install packages
+- if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then wget http://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
+  -O miniconda.sh; else wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
+  -O miniconda.sh; fi
+- chmod +x miniconda.sh
+- "./miniconda.sh -b"
+- if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then export PATH=/home/travis/miniconda2/bin:$PATH; else export PATH=/home/travis/miniconda3/bin:$PATH; fi
+- if $INSTALL_DEB_DEPENDECIES; then sudo rm -rf /dev/shm; fi
+- if $INSTALL_DEB_DEPENDECIES; then sudo ln -s /run/shm /dev/shm; fi
+- bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh)
+- sudo apt-get update
+- sudo apt-get install xvfb
+- if $INSTALL_DEB_DEPENDECIES; then travis_retry sudo apt-get install -qq --no-install-recommends
+  fsl afni elastix; fi
+- if $INSTALL_DEB_DEPENDECIES; then travis_retry sudo apt-get install -qq fsl-atlases;
+  fi
+- if $INSTALL_DEB_DEPENDECIES; then source /etc/fsl/fsl.sh; fi
+- if $INSTALL_DEB_DEPENDECIES; then source /etc/afni/afni.sh; fi
+- export FSLOUTPUTTYPE=NIFTI_GZ
+# Install vtk and fix numpy installation problem
+# Fix numpy problem: https://github.com/enthought/enable/issues/34#issuecomment-2029381
+- if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then travis_retry sudo apt-get install -qq libx11-dev swig;
+  echo '[x11]' >> $HOME/.numpy-site.cfg; 
+  echo 'library_dirs = /usr/lib64:/usr/lib:/usr/lib/x86_64-linux-gnu' >> $HOME/.numpy-site.cfg;
+  echo 'include_dirs = /usr/include:/usr/include/X11' >> $HOME/.numpy-site.cfg;
+  fi
 install:
-  - conda update --yes conda
-  - conda create -n testenv --yes pip python=$TRAVIS_PYTHON_VERSION
-  - source activate testenv
-  - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then pip install ordereddict; fi
-  - conda install --yes numpy scipy nose traits networkx dateutil
-  - pip install nibabel --use-mirrors
-  - pip install python-coveralls --use-mirrors
-  - pip install nose-cov --use-mirrors
-  - pip install https://github.com/RDFLib/rdflib/archive/master.zip
-  - pip install https://github.com/trungdong/prov/archive/rdf.zip
-  - python setup.py install
-
-# Run test
+- sudo apt-get install fusefat
+- conda update --yes conda
+- conda create -n testenv --yes pip python=$TRAVIS_PYTHON_VERSION
+- source activate testenv
+- if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then pip install ordereddict; fi
+- conda install --yes numpy scipy nose networkx python-dateutil
+- if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then conda install --yes traits; else pip install traits; fi
+- if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then conda install --yes vtk; fi
+- pip install python-coveralls
+- pip install nose-cov
+# Add tvtk (PIL is required by blockcanvas)
+# Install mayavi (see https://github.com/enthought/mayavi/issues/271)
+- if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then
+  pip install http://effbot.org/downloads/Imaging-1.1.7.tar.gz;
+  pip install -e git+https://github.com/enthought/etsdevtools.git#egg=etsdevtools;
+  pip install -e git+https://github.com/enthought/blockcanvas.git#egg=blockcanvas;
+  pip install -e git+https://github.com/enthought/etsproxy.git#egg=etsproxy;
+  pip install https://github.com/dmsurti/mayavi/archive/4d4aaf315a29d6a86707dd95149e27d9ed2225bf.zip;
+  pip install -e git+https://github.com/enthought/ets.git#egg=ets;
+  fi
+- pip install -e .
 script:
-  - nosetests --with-doctest --with-cov --cov nipype --cov-config .coveragerc --logging-level=INFO
-
-# Calculate coverage
+- python -W once:FSL:UserWarning:nipype `which nosetests` --with-doctest --with-cov --cover-package nipype --cov-config .coveragerc --logging-level=DEBUG --verbosity=3
 after_success:
-  - coveralls --config_file .coveragerc
+- coveralls --config_file .coveragerc
+deploy:
+  provider: pypi
+  user: satra
+  password:
+    secure: OCO0FXb4f+pH4Uw7zWCIRp3qOJ1t7rhky4K8MjNU8tyVCJgd6O/Bv8GJgceS0LktPodlAAjB8SxAhTORPAQZ1D/44PJYy3NQIisvej1zjLpaA9TEGfl6W7MqhDpRyMHW+cnSi/n84SAmdr+Z4vOxScDHdwr13EPmGyOIlHMAGnE=
+  on:
+    tags: true
+    repo: nipy/nipype
+    branch: master
+  distributions: "sdist bdist_wheel"

CHANGES

@@ -1,8 +1,79 @@
-Next release
+Release 0.12.0-rc1 (April 20, 2016)
 ============
 
+* FIX: Selecting "gamma" in FSL Level1Design now does what the name says (https://github.com/nipy/nipype/pull/1500)
+* ENH: Added grad_dev input to fsl.dti.bedpostx5 interface(https://github.com/nipy/nipype/pull/1493)
+* ENH: ResourceMultiProc plugin to support resource allocation (https://github.com/nipy/nipype/pull/1372)
+* ENH: Added dcm2niix interface (https://github.com/nipy/nipype/pull/1435)
+* ENH: Add nipype_crash_search command (https://github.com/nipy/nipype/pull/1422)
+* ENH: Created interface for BrainSuite Cortical Surface Extraction command line tools (https://github.com/nipy/nipype/pull/1305)
+* FIX: job execution on systems/approaches where locale is undefined (https://github.com/nipy/nipype/pull/1401)
+* FIX: Clean up byte/unicode issues using subprocess (https://github.com/nipy/nipype/pull/1394)
+* FIX: Prevent crash when tvtk is loaded - ETS_TOOLKIT=null (https://github.com/nipy/nipype/pull/973)
+* ENH: New interfaces in dipy: RESTORE, EstimateResponseSH, CSD and StreamlineTractography
+       (https://github.com/nipy/nipype/pull/1090)
+* ENH: Added interfaces of AFNI (https://github.com/nipy/nipype/pull/1360,
+       https://github.com/nipy/nipype/pull/1361, https://github.com/nipy/nipype/pull/1382)
+* ENH: Provides a Nipype wrapper for antsJointFusion (https://github.com/nipy/nipype/pull/1351)
+* ENH: Added support for PETPVC (https://github.com/nipy/nipype/pull/1335)
+* ENH: Merge S3DataSink into DataSink, added AWS documentation (https://github.com/nipy/nipype/pull/1316)
+* TST: Cache APT in CircleCI (https://github.com/nipy/nipype/pull/1333)
+* ENH: Add new flags to the BRAINSABC for new features (https://github.com/nipy/nipype/pull/1322)
+* ENH: Provides a Nipype wrapper for ANTs DenoiseImage (https://github.com/nipy/nipype/pull/1291)
+* FIX: Minor bugfix logging hash differences (https://github.com/nipy/nipype/pull/1298)
+* FIX: Use released Prov python library (https://github.com/nipy/nipype/pull/1279)
+* ENH: Support for Python 3 (https://github.com/nipy/nipype/pull/1221)
+* FIX: VTK version check missing when using tvtk (https://github.com/nipy/nipype/pull/1219)
+* ENH: Added an OAR scheduler plugin (https://github.com/nipy/nipype/pull/1259)
+* ENH: New ANTs interface: antsBrainExtraction (https://github.com/nipy/nipype/pull/1231)
+* API: Default model level for the bedpostx workflow has been set to "2" following FSL 5.0.9 lead
+* ENH: New interfaces for interacting with AWS S3: S3DataSink and S3DataGrabber (https://github.com/nipy/nipype/pull/1201)
+* ENH: Interfaces for MINC tools (https://github.com/nipy/nipype/pull/1304)
+* FIX: Use realpath to determine hard link source (https://github.com/nipy/nipype/pull/1388)
+* FIX: Correct linking/copying fallback behavior (https://github.com/nipy/nipype/pull/1391)
+* ENH: Nipype workflow and interfaces for FreeSurfer's recon-all (https://github.com/nipy/nipype/pull/1326)
+* FIX: Permit relative path for concatenated_file input to Concatenate() (https://github.com/nipy/nipype/pull/1411)
+* ENH: Makes ReconAll workflow backwards compatible with FreeSurfer 5.3.0 (https://github.com/nipy/nipype/pull/1434)
+* ENH: Added interfaces for AFNI 3dDegreeCentrality, 3dECM, 3dLFCD, 3dClipLevel, 3dmask_tool, and 3dSeg
+       (https://github.com/nipy/nipype/pull/1460)
+
+Release 0.11.0 (September 15, 2015)
+============
+
+* API: Change how hash values are computed (https://github.com/nipy/nipype/pull/1174)
+* ENH: New algorithm: mesh.WarpPoints applies displacements fields to point sets
+       (https://github.com/nipy/nipype/pull/889).
+* 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)
+* ENH: dipy.TrackDensityMap interface now accepts a reference image (https://github.com/nipy/nipype/pull/1091)
+* 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)
+* FIX: Updates to SGE Plugins
+    (https://github.com/nipy/nipype/pull/1129)
+* ENH: Add ants JointFusion() node with testing
+    (https://github.com/nipy/nipype/pull/1160)
+* ENH: Add --float option for antsRegistration calls
+    (https://github.com/nipy/nipype/pull/1159)
+* ENH: Added interface to simulate DWIs using the multi-tensor model
+       (https://github.com/nipy/nipype/pull/1085)
+* ENH: New interface for FSL fslcpgeom utility (https://github.com/nipy/nipype/pull/1152)
+* ENH: Added SLURMGraph plugin for submitting jobs to SLURM with dependencies (https://github.com/nipy/nipype/pull/1136)
+* FIX: Enable absolute path definitions in DCMStack (https://github.com/nipy/nipype/pull/1089,
+       replaced by https://github.com/nipy/nipype/pull/1093)
+* ENH: New mesh.MeshWarpMaths to operate on surface-defined warpings
+       (https://github.com/nipy/nipype/pull/1016)
+* FIX: Refactor P2PDistance, change name to ComputeMeshWarp, add regression tests,
+       fix bug in area weighted distance, and added optimizations
+       (https://github.com/nipy/nipype/pull/1016)
+* ENH: Add an option not to resubmit Nodes that finished running when using SGEGraph (https://github.com/nipy/nipype/pull/1002)
+* FIX: FUGUE is now properly listing outputs. (https://github.com/nipy/nipype/pull/978)
 * ENH: Improved FieldMap-Based (FMB) workflow for correction of susceptibility distortions in EPI seqs.
        (https://github.com/nipy/nipype/pull/1019)
+* FIX: In the FSLXcommand _list_outputs function fixed for loop range (https://github.com/nipy/nipype/pull/1071)
 * ENH: Dropped support for now 7 years old Python 2.6 (https://github.com/nipy/nipype/pull/1069)
 * FIX: terminal_output is not mandatory anymore (https://github.com/nipy/nipype/pull/1070)
 * ENH: Added "nipype_cmd" tool for running interfaces from the command line (https://github.com/nipy/nipype/pull/795)
@@ -42,6 +113,15 @@ Next release
 * ENH: Usability improvements in cluster environments (https://github.com/nipy/nipype/pull/1025)
 * ENH: ANTs JointFusion() (https://github.com/nipy/nipype/pull/1042)
 * ENH: Added csvReader() utility (https://github.com/nipy/nipype/pull/1044)
+* FIX: typo in nipype.interfaces.freesurfer.utils.py Tkregister2 (https://github.com/nipy/nipype/pull/1083)
+* FIX: SSHDataGrabber outputs now return full path to the grabbed/downloaded files. (https://github.com/nipy/nipype/pull/1086)
+* FIX: Add QA output for TSNR to resting workflow (https://github.com/nipy/nipype/pull/1088)
+* FIX: Change N4BiasFieldCorrection to use short tag for dimensionality (backward compatible) (https://github.com/nipy/nipype/pull/1096)
+* ENH: Added -newgrid input to Warp in AFNI (3dWarp wrapper) (https://github.com/nipy/nipype/pull/1128)
+* FIX: Fixed AFNI Copy interface to use positional inputs as required (https://github.com/nipy/nipype/pull/1131)
+* ENH: Added a check in Dcm2nii to check if nipype created the config.ini file and remove if true (https://github.com/nipy/nipype/pull/1132)
+* ENH: Use a while loop to wait for Xvfb (up to a max wait time "xvfb_max_wait" in config file, default 10)
+       (https://github.com/nipy/nipype/pull/1142)
 
 Release 0.10.0 (October 10, 2014)
 ============

CONTRIBUTING.md

@@ -10,16 +10,22 @@
 * Pull Requests should be tested, if feasible:
     - bugfixes should include regression tests
     - new behavior should at least get minimal exercise
-* Use a descriptive prefix for your PR: ENH, FIX, TST, DOC, STY, REF (refactor), WIP (Work in progress)
-* After submiting the PR, include an update to the CHANGES file: prefix: description (URL of pull request)
+* Use a descriptive prefix for your PR: ENH (enhancement), FIX, TST, DOC, STY, REF (refactor), WIP (Work in progress)
+* After submitting the PR, include an update to the CHANGES file: prefix: description (URL of pull request)
 * `make specs`
 * do: `make check-before-commit` before submitting the PR. This will require you to either install or be in developer mode with: `python setup.py install/develop`.
+* In general, do not catch exceptions without good reason. 
+  * catching non-fatal exceptions. 
+    Log the exception as a warning.
+  * adding more information about what may have caused the error.
+    Raise a new exception using ``raise_from(NewException("message"), oldException)`` from ``future``.
+    Do not log this, as it creates redundant/confusing logs.
 
 ## Contributing issues
 
 When opening a new Issue, please take the following steps:
 
-1. Search GitHub and/or [Neurostars](neurostars.org) for your issue to avoid duplicate reports.
+1. Search GitHub and/or [Neurostars](http://neurostars.org) for your issue to avoid duplicate reports.
    Keyword searches for your error messages are most helpful.
 2. If possible, try updating to master and reproducing your issue,
    because we may have already fixed it.

LICENSE

@@ -1,30 +1,15 @@
-Copyright (c) 2009-2014, NIPY Developers
-All rights reserved.
+Copyright (c) 2009-2016, Nipype developers
 
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are
-met:
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
 
-    * Redistributions of source code must retain the above copyright
-       notice, this list of conditions and the following disclaimer.
+    http://www.apache.org/licenses/LICENSE-2.0
 
-    * Redistributions in binary form must reproduce the above
-       copyright notice, this list of conditions and the following
-       disclaimer in the documentation and/or other materials provided
-       with the distribution.
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
 
-    * Neither the name of the NIPY Developers nor the names of any
-       contributors may be used to endorse or promote products derived
-       from this software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
-"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
-LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
-A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
-OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
-SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
-LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
-DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
-THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+Prior to release 0.12, Nipype was licensed under a BSD license.

MANIFEST.in

@@ -10,5 +10,4 @@ include doc/documentation.zip
 include nipype/COMMIT_INFO.txt
 
 recursive-include doc *
-recursive-include matlabscripts *
 recursive-include tools *

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
 
@@ -13,8 +15,6 @@ sdist: zipdoc
 	python setup.py sdist
 	@echo "Done building source distribution."
 	# XXX copy documentation.zip to dist directory.
-	# XXX Somewhere the doc/_build directory is removed and causes
-	# this script to fail.
 
 egg: zipdoc
 	@echo "Building egg..."
@@ -26,7 +26,7 @@ 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
 
@@ -43,7 +43,10 @@ clean-build:
 clean-ctags:
 	rm -f tags
 
-clean: clean-build clean-pyc clean-so clean-ctags
+clean-doc:
+	rm -rf doc/_build
+
+clean: clean-build clean-pyc clean-so clean-ctags clean-doc
 
 in: inplace # just a shortcut
 inplace:
@@ -64,12 +67,13 @@ test: clean test-code
 
 html:
 	@echo "building docs"
-	make -C doc clean html
+	make -C doc clean htmlonly
 
 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"