FIX: Conflict correction after merge with master

Author: miykael

.travis.yml

@@ -8,12 +8,12 @@ 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
+- 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 [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then export PATH=/home/travis/miniconda/bin:$PATH; else export PATH=/home/travis/miniconda3/bin:$PATH; fi
+- 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);

CHANGES

@@ -1,5 +1,8 @@
 Next Release
 ============
+
+* 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)
 

circle.yml

@@ -15,7 +15,7 @@ dependencies:
     - 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/feeds ]]; then wget "http://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-5.0.9-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

doc/users/plugins.rst

@@ -9,7 +9,7 @@ available plugins allow local and distributed execution of workflows and
 debugging. Each available plugin is described below.
 
 Current plugins are available for Linear, Multiprocessing, IPython_ distributed
-processing platforms and for direct processing on SGE_, PBS_, HTCondor_, LSF_, and SLURM_. We
+processing platforms and for direct processing on SGE_, PBS_, HTCondor_, LSF_, OAR_, and SLURM_. We
 anticipate future plugins for the Soma_ workflow.
 
 .. note::
@@ -276,6 +276,34 @@ for all nodes could look like this::
                          wrapper_args=shim_args)
         )
 
+OAR
+---
+
+In order to use nipype with OAR_ you simply need to call::
+
+       workflow.run(plugin='OAR')
+
+Optional arguments::
+
+  template: custom template file to use
+  oar_args: any other command line args to be passed to qsub.
+  max_jobname_len: (PBS only) maximum length of the job name.  Default 15.
+
+For example, the following snippet executes the workflow on myqueue with
+a custom template::
+
+       workflow.run(plugin='oar',
+          plugin_args=dict(template='mytemplate.sh', oarsub_args='-q myqueue')
+
+In addition to overall workflow configuration, you can use node level
+configuration for OAR::
+
+    node.plugin_args = {'oarsub_args': '-l "nodes=1/cores=3"'}
+
+this would apply only to the node and is useful in situations, where a
+particular node might use more resources than other nodes in a workflow.
+
+
 ``qsub`` emulation
 ~~~~~~~~~~~~~~~~~~
 

nipype/interfaces/ants/__init__.py

@@ -11,7 +11,7 @@
 
 
 # Segmentation Programs
-from .segmentation import Atropos, LaplacianThickness, N4BiasFieldCorrection, JointFusion
+from .segmentation import Atropos, LaplacianThickness, N4BiasFieldCorrection, JointFusion, antsCorticalThickness, antsBrainExtraction
 
 # Visualization Programs
 from .visualization import ConvertScalarImageToRGB, CreateTiledMosaic