Added grad_dev input to BEDPOSTX5 interface

Author: mattfeld

.gitignore

@@ -5,6 +5,7 @@
 /nipype/build
 /nipype/nipype.egg-info
 /doc/_build
+/doc/preproc
 /doc/users/examples
 /doc/api/generated
 *.pyc
@@ -17,3 +18,10 @@
 .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

.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

@@ -3,39 +3,62 @@ cache:
 language: python
 python:
 - 2.7
+- 3.4
+- 3.5
 env:
 - 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
+- if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then wget http://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
+  -O miniconda.sh; else wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
   -O miniconda.sh; fi
 - chmod +x miniconda.sh
 - "./miniconda.sh -b"
-- export PATH=/home/travis/miniconda/bin:$PATH
+- 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
-- if $INSTALL_DEB_DEPENDECIES; then bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh);
-  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' >> $HOME/.numpy-site.cfg;
+  fi
 install:
+- sudo apt-get install fusefat
 - conda update --yes conda
 - conda create -n testenv --yes pip python=$TRAVIS_PYTHON_VERSION
 - source activate testenv
 - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then pip install ordereddict; fi
-- conda install --yes numpy scipy nose traits networkx dateutil
-- pip install nibabel
+- 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
-- pip install https://github.com/RDFLib/rdflib/archive/master.zip
-- pip install https://github.com/trungdong/prov/archive/rdf.zip
+# 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 -r requirements.txt  # finish remaining requirements
 - python setup.py install
 script:
-- nosetests --with-doctest --with-cov --cov nipype --cov-config .coveragerc --logging-level=INFO
+- 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
 deploy:

CHANGES

@@ -1,6 +1,40 @@
-Next Release
+Release 0.12.0-rc1 (April 20, 2016)
 ============
 
+* 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)
 ============
 

CONTRIBUTING.md

@@ -19,7 +19,7 @@
 
 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.

Makefile

@@ -15,8 +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..."
@@ -45,7 +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:
@@ -66,7 +67,7 @@ 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"

README.rst

@@ -34,6 +34,10 @@ NIPYPE: Neuroimaging in Python: Pipelines and Interfaces
     :target: https://pypi.python.org/pypi/nipype/
     :alt: License
 
+.. image:: https://img.shields.io/badge/gitter-join%20chat%20%E2%86%92-brightgreen.svg?style=flat
+    :target: http://gitter.im/nipy/nipype
+    :alt: Chat
+
 Current neuroimaging software offer users an incredible opportunity to
 analyze data using a variety of different algorithms. However, this has
 resulted in a heterogeneous collection of specialized applications

THANKS.rst

@@ -1,100 +1,22 @@
 .. -*- mode: rst -*-
 
-
 Code contributors
 -----------------
-Contributors to Nipype include but are not limited to:
-
-.. hlist::
 
-  * Aimi Watanabe
-  * Alexander Schaefer
-  * Alexandre Gramfort
-  * Anisha Keshavan
-  * Ariel Rokem
-  * Ben Acland
-  * Basile Pinsard
-  * Brendan Moloney
-  * Brian Cheung
-  * Charl Linssen
-  * Chris Filo Gorgolewski
-  * Chris Steele
-  * Christian Haselgrove
-  * Christopher Burns
-  * Cindee Madison
-  * Claire Tarbert
-  * Colin Buchanan
-  * Daniel Ginsburg
-  * Daniel Haehn
-  * Daniel Margulies
-  * Dav Clark
-  * David Welch
-  * Drew Erickson
-  * Erik Kastman
-  * Félix C. Morency
-  * Gael Varoquaux
-  * Hans Johnson
-  * Janosch Linkersdörfer
-  * Januzz
-  * Jarrod Millman
-  * Jeff Lai
-  * Jessica Forbes
-  * John Salvatore
-  * Lijie Huang
-  * Michael Hallquist
-  * Michael Hanke
-  * Michael Notter
-  * Michael Waskom
-  * Nolan Nichols
-  * Oliver Hinds
-  * Oscar Esteban
-  * Rosalia Tungaraza
-  * Satrajit Ghosh
-  * Sharad Sikka
-  * Stephan Gerhard
-  * Erik Ziegler
-  * Valentin Haenel
-  * Xiangzhen Kong
-  * Xu Wang
-  * Yannick Schwartz
-  * Yaroslav O. Halchenko
+See `Github contributors list <https://github.com/nipy/nipype/graphs/contributors>`__.
 
-For full most up to date list see `Ohloh <https://www.ohloh.net/p/nipype/contributors>`__.
+Funding
+-------
 
-Other contributors
-------------------
+Nipype is currently supported by `1R01EB020740-01A1 Nipype: Dataflows for Reproducible Biomedical Research <https://projectreporter.nih.gov/project_info_description.cfm?aid=9053094>`__.
 
-.. hlist::
+Satrajit Ghosh work on this project was partially funded by NIBIB `R03EB008673 <https://projectreporter.nih.gov/project_info_description.cfm?aid=7501200>`__ and by the `INCF <http://www.incf.org>`__ through a contract with TankThink Labs, LLC.
+Chris Burns was supported by NIMH grant `5R01MH081909-02  Continued Development and Maintenance of the Neuroimaging in Python Project <https://projectreporter.nih.gov/project_info_description.cfm?aid=7288112>`__. 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>`__,
+`S10 RR023392	 Enterprise Storage In A Collaborative Neuroimaging Environment	 <http://projectreporter.nih.gov/project_info_description.cfm?aid=7209718>`__,
+`R01 NS040068	 Neurobiological Predictors of Huntington's Disease	 <http://projectreporter.nih.gov/project_info_description.cfm?aid=6266377>`__,
+and `UL1 TR000442	University of Iowa Clinical and Translational Science Program <http://projectreporter.nih.gov/project_info_description.cfm?aid=8467220>`__.
 
-  * Matthew Brett
-  * Michael Castelle
-  * Philippe Ciuciu
-  * Yann Cointepas
-  * Mark D'Esposito
-  * Susan Gabrieli
-  * Brian Hawthorne
-  * Tim Leslie
-  * Fernando Perez
-  * Tyler Perrachione
-  * Jean-Baptiste Poline
-  * Alexis Roche
-  * Denis Riviere
-  * Gretchen Reynolds
-  * Jonathan Taylor
-  * Bertrand Thirion
-  * Bernjamin Thyreau
-  * 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>`__,
-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>`__.
-

Vagrantfile

@@ -20,19 +20,20 @@ $script = <<SCRIPT
 # qconf -aattr queue slots "2, [neuro=3]" main.q
 
 # install anaconda
-wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh
+wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
 chmod +x miniconda.sh
 ./miniconda.sh -b
-echo "export PATH=$HOME/miniconda/bin:\\$PATH" >> .bashrc
+echo "export PATH=$HOME/miniconda3/bin:\\$PATH" >> .bashrc
 
 # install nipype dependencies
-$HOME/miniconda/bin/conda update --yes conda
-$HOME/miniconda/bin/conda install --yes pip numpy scipy nose traits networkx
-$HOME/miniconda/bin/conda install --yes dateutil ipython-notebook matplotlib
-$HOME/miniconda/bin/pip install nibabel --use-mirrors
-$HOME/miniconda/bin/pip install https://github.com/RDFLib/rdflib/archive/master.zip
-$HOME/miniconda/bin/pip install https://github.com/trungdong/prov/archive/rdf.zip
-$HOME/miniconda/bin/pip install https://github.com/nipy/nipype/archive/master.zip
+$HOME/miniconda3/bin/conda update --yes conda
+$HOME/miniconda3/bin/conda install --yes pip scipy nose networkx lxml future simplejson
+$HOME/miniconda3/bin/conda install --yes python-dateutil jupyter matplotlib
+$HOME/miniconda3/bin/pip install nibabel
+$HOME/miniconda3/bin/pip install prov
+$HOME/miniconda3/bin/pip install xvfbwrapper
+$HOME/miniconda3/bin/pip install traits
+$HOME/miniconda3/bin/pip install https://github.com/nipy/nipype/archive/master.zip
 SCRIPT
 
 Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|