Merge branch 'oar_support' of https://github.com/demianw/nipype into oar_support

Author: demianw

.gitignore

@@ -14,3 +14,6 @@
 .pydevproject
 .idea/
 /documentation.zip
+.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

@@ -1,42 +1,50 @@
 cache:
-  - apt
+- apt
 language: python
 python:
-  - 2.7
+- 2.7
 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 [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh
+  -O miniconda.sh; else wget http://repo.continuum.io/miniconda/Miniconda3-3.6.0-Linux-x86_64.sh
+  -O miniconda.sh; fi
+- chmod +x miniconda.sh
+- "./miniconda.sh -b"
+- export PATH=/home/travis/miniconda/bin:$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 $INSTALL_DEB_DEPENDECIES; then source /etc/fsl/fsl.sh; fi
 install:
-  - conda update --yes conda
-  - conda create -n testenv --yes pip python=$TRAVIS_PYTHON_VERSION
-  - source activate testenv
-  - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then pip install ordereddict; fi
-  - conda install --yes numpy scipy nose traits networkx dateutil
-  - pip install nibabel --use-mirrors
-  - pip install python-coveralls --use-mirrors
-  - pip install nose-cov --use-mirrors
-  - pip install https://github.com/RDFLib/rdflib/archive/master.zip
-  - pip install https://github.com/trungdong/prov/archive/rdf.zip
-  - python setup.py install
-
-# Run test
+- conda update --yes conda
+- conda create -n testenv --yes pip python=$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
+- 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
+- python setup.py install
 script:
-  - nosetests --with-doctest --with-cov --cov nipype --cov-config .coveragerc --logging-level=INFO
-
-# Calculate coverage
+- nosetests --with-doctest --with-cov --cov nipype --cov-config .coveragerc --logging-level=INFO
 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

@@ -1,6 +1,35 @@
-Next release
+Next Release
 ============
+* 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)
 
+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,
@@ -10,6 +39,7 @@ Next release
 * 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)
@@ -51,6 +81,13 @@ Next release
 * 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)
 ============

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
 
@@ -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

@@ -5,26 +5,32 @@ 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://pypip.in/version/nipype/badge.png
+.. 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
 
-.. image:: https://pypip.in/download/nipype/badge.png
+.. image:: https://img.shields.io/pypi/dm/nipype.svg
     :target: https://pypi.python.org/pypi/nipype/
     :alt: Downloads
 
-.. image:: https://pypip.in/py_versions/nipype/badge.png
+.. image:: https://img.shields.io/pypi/pyversions/nipype.svg
     :target: https://pypi.python.org/pypi/nipype/
     :alt: Supported Python versions
 
-.. image:: https://pypip.in/status/nipype/badge.png
+.. image:: https://img.shields.io/pypi/status/nipype.svg
     :target: https://pypi.python.org/pypi/nipype/
     :alt: Development Status
 
-.. image:: https://pypip.in/license/nipype/badge.png
+.. image:: https://img.shields.io/pypi/l/nipype.svg
     :target: https://pypi.python.org/pypi/nipype/
     :alt: License
 
@@ -64,7 +70,7 @@ Website
 -------
 
 Information specific to Nipype is located here::
-	    
+
     http://nipy.org/nipype
 
 
@@ -75,12 +81,12 @@ 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 discussion please use the following mailing list::
-       
-       http://projects.scipy.org/mailman/listinfo/nipy-devel
-	   
+
+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
@@ -124,5 +130,5 @@ There are interfaces to some GNU code but these are entirely optional.
 All trademarks referenced herein are property of their respective
 holders.
 
-Copyright (c) 2009-2014, NIPY Developers
+Copyright (c) 2009-2015, NIPY Developers
 All rights reserved.

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>`__.
 

bin/nipype2boutiques

@@ -0,0 +1,8 @@
+#!/usr/bin/env python
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+import sys
+from nipype.utils.nipype2boutiques import main
+
+if __name__ == '__main__':
+    main(sys.argv)

circle.yml

@@ -0,0 +1,83 @@
+dependencies:
+  cache_directories:
+    - "~/examples/data"
+    - "~/examples/fsdata"
+    - "~/examples/feeds"
+    - "~/mcr"
+    - "~/spm12"
+    - "~/fsl"
+    - "~/examples/fsl_course_data"
+  override:
+    - pip install --upgrade pip
+    - pip install -e .
+    - pip install matplotlib sphinx ipython boto
+    - gem install fakes3
+    - if [[ ! -d ~/fsl ]]; then wget "http://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-5.0.9-centos6_64.tar.gz"; tar zxvf fsl-5.0.9-centos6_64.tar.gz; mv fsl ~/fsl; fi
+    - if [[ ! -d ~/examples/data ]]; then wget "http://tcpdiag.dl.sourceforge.net/project/nipy/nipype/nipype-0.2/nipype-tutorial.tar.bz2"; tar jxvf nipype-tutorial.tar.bz2; mkdir ~/examples; mv nipype-tutorial/* ~/examples/; fi
+    # we download this manually because CircleCI does not cache apt
+    - if [[ ! -d ~/examples/feeds ]]; then wget "http://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-5.0.8-feeds.tar.gz"; tar zxvf fsl-5.0.8-feeds.tar.gz; mv feeds ~/examples/; fi
+    - if [[ ! -d ~/examples/fsl_course_data ]]; then wget -c "http://fsl.fmrib.ox.ac.uk/fslcourse/fdt1.tar.gz" ; wget -c "http://fsl.fmrib.ox.ac.uk/fslcourse/fdt2.tar.gz"; wget -c "http://fsl.fmrib.ox.ac.uk/fslcourse/tbss.tar.gz"; mkdir ~/examples/fsl_course_data; tar zxvf fdt1.tar.gz -C ~/examples/fsl_course_data; tar zxvf fdt2.tar.gz -C ~/examples/fsl_course_data; tar zxvf tbss.tar.gz -C ~/examples/fsl_course_data; fi
+    - bash ~/nipype/tools/install_spm_mcr.sh
+    - 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:
+    - nosetests --with-doctest --logging-level=DEBUG --verbosity=3:
+        environment:
+          SPMMCRCMD: "$HOME/spm12/run_spm12.sh $HOME/mcr/v85/ script"
+          FORCE_SPMMCR: 1
+          FSL_COURSE_DATA: "$HOME/examples/fsl_course_data"
+          FSLDIR: "$HOME/fsl/"
+          PATH: "$HOME/fsl/bin:$PATH"
+          LD_LIBRARY_PATH: "$HOME/fsl/lib"
+          FSLOUTPUTTYPE: "NIFTI_GZ"
+        timeout: 2600
+    - set -o pipefail && cd doc && make html 2>&1 | tee ~/log.txt
+    - cat ~/log.txt && if grep -q "ERROR" ~/log.txt; then false; else true; fi
+    - python ~/nipype/tools/run_examples.py test_spm Linear workflow3d workflow4d:
+        pwd: ../examples
+        environment:
+          SPMMCRCMD: "$HOME/spm12/run_spm12.sh $HOME/mcr/v85/ script"
+          FORCE_SPMMCR: 1
+          FSLDIR: "$HOME/fsl/"
+          PATH: "$HOME/fsl/bin:$PATH"
+          LD_LIBRARY_PATH: "$HOME/fsl/lib"
+          FSLOUTPUTTYPE: "NIFTI_GZ"
+        timeout: 1600
+    - python ~/nipype/tools/run_examples.py fmri_fsl_feeds Linear l1pipeline:
+        pwd: ../examples
+        environment:
+          FSLDIR: "$HOME/fsl/"
+          PATH: "$HOME/fsl/bin:$PATH"
+          LD_LIBRARY_PATH: "$HOME/fsl/lib"
+          FSLOUTPUTTYPE: "NIFTI_GZ"
+    - python ~/nipype/tools/run_examples.py fmri_spm_dartel Linear level1 l2pipeline:
+        pwd: ../examples
+        environment:
+          SPMMCRCMD: "$HOME/spm12/run_spm12.sh $HOME/mcr/v85/ script"
+          FORCE_SPMMCR: 1
+          FSLDIR: "$HOME/fsl/"
+          PATH: "$HOME/fsl/bin:$PATH"
+          LD_LIBRARY_PATH: "$HOME/fsl/lib"
+          FSLOUTPUTTYPE: "NIFTI_GZ"
+        timeout: 1600
+    - python ~/nipype/tools/run_examples.py fmri_fsl_reuse Linear level1_workflow:
+        pwd: ../examples
+        environment:
+          FSLDIR: "$HOME/fsl/"
+          PATH: "$HOME/fsl/bin:$PATH"
+          LD_LIBRARY_PATH: "$HOME/fsl/lib"
+          FSLOUTPUTTYPE: "NIFTI_GZ"
+    - python ~/nipype/tools/run_examples.py fmri_spm_nested Linear level1 l2pipeline:
+        pwd: ../examples
+        environment:
+          SPMMCRCMD: "$HOME/spm12/run_spm12.sh $HOME/mcr/v85/ script"
+          FORCE_SPMMCR: 1
+          FSLDIR: "$HOME/fsl/"
+          PATH: "$HOME/fsl/bin:$PATH"
+          LD_LIBRARY_PATH: "$HOME/fsl/lib"
+          FSLOUTPUTTYPE: "NIFTI_GZ"
+
+general:
+  artifacts:
+    - "doc/_build/html"
+    - "~/log.txt"