Merge branch 'master' of https://github.com/nipy/nipype

Author: jason-wg

.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

@@ -16,22 +16,43 @@ before_install:
 - 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' >> $HOME/.numpy-site.cfg;
+  fi
 install:
 - conda update --yes conda
 - conda create -n testenv --yes pip python=$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 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 -r requirements.txt  # finish remaining requirements
 - python setup.py install
 script:

CHANGES

@@ -1,6 +1,19 @@
 Next release
 ============
 
+* 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)
@@ -9,7 +22,8 @@ Next release
 * 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)
 
 Release 0.11.0 (September 15, 2015)
 ============

bin/nipype2boutiques

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!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

bin/nipype_cmd

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!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

bin/nipype_display_crash

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!python
 """Displays crash information from Nipype crash files. For certain crash files,
 one can rerun a failed node in a temp directory.
 

circle.yml

@@ -1,83 +1,77 @@
 dependencies:
   cache_directories:
+    - "~/.apt-cache"
     - "~/examples/data"
     - "~/examples/fsdata"
-    - "~/examples/feeds"
     - "~/mcr"
     - "~/spm12"
-    - "~/fsl"
     - "~/examples/fsl_course_data"
+  pre:
+    # Let CircleCI cache the apt archive
+    - sudo rm -rf /var/cache/apt/archives && sudo ln -s ~/.apt-cache /var/cache/apt/archives && mkdir -p ~/.apt-cache/partial
+    - bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh)
   override:
+    # Install apt packages
+    - sudo apt-get install -y fsl-core fsl-atlases fsl-mni152-templates fsl-feeds afni swig python-vtk xvfb
+    - echo 'source /etc/fsl/fsl.sh' >> $HOME/.profile
+    - echo 'source /etc/afni/afni.sh' >> $HOME/.profile
+    - mkdir -p ~/examples/ && ln -sf /usr/share/fsl-feeds/ ~/examples/feeds
+    # Enable system-wide vtk
+    - ln -sf /usr/lib/pymodules/python2.7/vtk ~/virtualenvs/venv-system/lib/python2.7/site-packages/
+    # Set up python environment
     - pip install --upgrade pip
     - pip install -e .
-    - pip install matplotlib sphinx ipython boto
+    - pip install matplotlib sphinx ipython boto coverage dipy
+    # Add tvtk
+    - 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 -e git+https://github.com/enthought/ets.git#egg=ets
     - 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-5.0.9-feeds.tar.gz"; tar zxvf fsl-5.0.9-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
+    - if [[ ! -d ~/examples/data ]]; then wget "https://dl.dropbox.com/s/jzgq2nupxyz36bp/nipype-tutorial.tar.bz2" && tar jxvf nipype-tutorial.tar.bz2 && mv nipype-tutorial/* ~/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
+    - 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
+machine:
+  environment:
+    FSLOUTPUTTYPE: NIFTI_GZ
 test:
   override:
-    - nosetests --with-doctest --logging-level=DEBUG --verbosity=3:
+    - mkdir -p ${CIRCLE_TEST_REPORTS}/nose
+    - source $HOME/.profile; nosetests --with-doctest --xunit-file="${CIRCLE_TEST_REPORTS}/nose/${CIRCLE_PROJECT_REPONAME}.xml" -c ./.noserc --logging-level=DEBUG --verbosity=3:
         environment:
           SPMMCRCMD: "$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:
+    - source $HOME/.profile; python ~/nipype/tools/run_examples.py test_spm Linear workflow3d workflow4d:
         pwd: ../examples
         environment:
           SPMMCRCMD: "$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:
+    - source $HOME/.profile; python ~/nipype/tools/run_examples.py fmri_fsl_feeds Linear l1pipeline:
         pwd: ../examples
-        environment:
-          FSLDIR: "$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:
+    - source $HOME/.profile; python ~/nipype/tools/run_examples.py fmri_spm_dartel Linear level1 l2pipeline:
         pwd: ../examples
         environment:
           SPMMCRCMD: "$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:
+    - source $HOME/.profile; python ~/nipype/tools/run_examples.py fmri_fsl_reuse Linear level1_workflow:
         pwd: ../examples
-        environment:
-          FSLDIR: "$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:
+    - source $HOME/.profile; python ~/nipype/tools/run_examples.py fmri_spm_nested Linear level1 l2pipeline:
         pwd: ../examples
         environment:
           SPMMCRCMD: "$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"
+    - "nosetests.xml"
+    - "coverage.xml"

doc/devel/cmd_interface_devel.rst

@@ -198,11 +198,13 @@ output_name (optional)
      name of the output (if this is not set same name as the input will be
      assumed)
 
-keep_extension (optional - not used)
-     if you want the extension from the input to be kept
+keep_extension (optional)
+     if you want the extension from the input or name_template to be kept. The
+     name_template extension always overrides the input extension.
 
 In addition one can add functionality to your class or base class, to allow
-changing extensions specific to package or interface
+changing extensions specific to package or interface. This overload function is
+trigerred only if keep_extension is not defined.
 
 .. testcode::
 

doc/documentation.rst

@@ -9,7 +9,7 @@ Documentation
    :Release: |version|
    :Date: |today|
 
-Previous versions:  `0.10.0 <http://nipy.org/nipype/0.10.0>`_ `0.9.2 <http://nipy.org/nipype/0.9.2>`_
+Previous versions:  `0.11.0 <http://nipy.org/nipype/0.11.0>`_ `0.10.0 <http://nipy.org/nipype/0.10.0>`_
 
 .. container:: doc2
 

doc/links_names.txt

@@ -46,7 +46,7 @@
 .. _pylint: http://www.logilab.org/project/pylint
 .. _pyflakes: http://divmod.org/trac/wiki/DivmodPyflakes
 .. _virtualenv: http://pypi.python.org/pypi/virtualenv
-.. _git: http://git.or.cz/
+.. _git: https://git-scm.com/
 .. _flymake: http://flymake.sourceforge.net/
 .. _rope: http://rope.sourceforge.net/
 .. _pymacs: http://pymacs.progiciels-bpi.ca/pymacs.html
@@ -60,21 +60,21 @@
 .. _`python coverage tester`: http://nedbatchelder.com/code/modules/coverage.html
 
 .. Other python projects
-.. _numpy: http://www.scipy.org/NumPy
+.. _numpy: http://www.numpy.org/
 .. _scipy: http://www.scipy.org
-.. _ipython: http://ipython.scipy.org
-.. _`ipython manual`: http://ipython.scipy.org/doc/manual/html
-.. _matplotlib: http://matplotlib.sourceforge.net
+.. _ipython: https://ipython.org
+.. _`ipython manual`: https://ipython.readthedocs.org/en/stable/
+.. _matplotlib: http://matplotlib.org/
 .. _ETS: http://code.enthought.com/projects/tool-suite.php
 .. _`Enthought Tool Suite`: http://code.enthought.com/projects/tool-suite.php
 .. _python: http://www.python.org
 .. _mayavi: http://mayavi.sourceforge.net/
-.. _sympy: http://code.google.com/p/sympy/
-.. _networkx: http://networkx.lanl.gov/
-.. _pythonxy: http://www.pythonxy.com/
+.. _sympy: http://www.sympy.org/
+.. _networkx: https://networkx.github.io/
+.. _pythonxy: https://python-xy.github.io/
 .. _EPD: http://www.enthought.com/products/epd.php
 .. _Traits: http://code.enthought.com/projects/traits/
-.. _Anaconda: https://store.continuum.io/cshop/anaconda/
+.. _Anaconda: https://www.continuum.io/downloads
 .. _Canopy: https://www.enthought.com/products/canopy/
 
 .. Python imaging projects