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

Author: jason-wg

.noserc

@@ -1,11 +1,10 @@
 [nosetests]
 verbosity=3
 
+logging-level=DEBUG
+with-doctest=1
+with-xunit=1
 with-coverage=1
 cover-branches=1
 cover-xml=1
-cover-xml-file=./coverage.xml
 cover-min-percentage=50
-
-
-with-xunit=1

CHANGES

@@ -1,5 +1,9 @@
-Release 0.12.0-rc2 (June 19, 2016)
-============
+Upcoming release 0.13
+=====================
+
+
+Release 0.12.0 (July 12, 2016)
+==============================
 
 * ENH: New interface for Bruker to Nifti converter (https://github.com/nipy/nipype/pull/1523)
 * FIX: output file naming for FIRST outputs (https://github.com/nipy/nipype/pull/1524)
@@ -41,7 +45,7 @@ Release 0.12.0-rc2 (June 19, 2016)
        (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
@@ -127,7 +131,7 @@ Release 0.11.0 (September 15, 2015)
        (https://github.com/nipy/nipype/pull/1142)
 
 Release 0.10.0 (October 10, 2014)
-============
+=================================
 
 * ENH: New miscelaneous interfaces: SplitROIs (mapper), MergeROIs (reducer)
        to enable parallel processing of very large images.
@@ -171,19 +175,19 @@ Release 0.10.0 (October 10, 2014)
 * FIX: Update for FSL 5.0.7 which deprecated Contrast Manager
 
 Release 0.9.2 (January 31, 2014)
-============
+================================
 
 * FIX: DataFinder was broken due to a typo
 * FIX: Order of DataFinder outputs was not guaranteed, it's human sorted now
 * ENH: New interfaces: Vnifti2Image, VtoMat
 
 Release 0.9.1 (December 25, 2013)
-============
+=================================
 
 * FIX: installation issues
 
 Release 0.9.0 (December 20, 2013)
-============
+=================================
 
 * ENH: SelectFiles: a streamlined version of DataGrabber
 * ENH: new tools for defining workflows: JoinNode, synchronize and itersource

Dockerfile

@@ -0,0 +1,74 @@
+# Copyright (c) 2016, The developers of the Stanford CRN
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+# * Redistributions of source code must retain the above copyright notice, this
+#   list of conditions and the following disclaimer.
+#
+# * 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.
+#
+# * Neither the name of crn_base nor the names of its
+#   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 HOLDER 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.
+
+FROM nipype/testnipypedata:latest
+MAINTAINER Stanford Center for Reproducible Neuroscience <[email protected]>
+
+# Preparations
+RUN ln -snf /bin/bash /bin/sh
+
+# Install this branch's code
+WORKDIR /root/src
+
+# Install matplotlib, sphinx and coverage to build documentation
+# and run tests with coverage
+RUN source activate nipypetests-2.7 && \
+    pip install matplotlib sphinx coverage && \
+    source activate nipypetests-3.4 && \
+    pip install matplotlib sphinx coverage && \
+    source activate nipypetests-3.5 && \
+    pip install matplotlib sphinx coverage
+
+ADD . nipype/
+
+# Install the checked out version of nipype, check that requirements are
+# installed and install it for each of the three environments.
+RUN cd nipype/ && \
+    source activate nipypetests-2.7 && \
+    pip install -r requirements.txt && \
+    pip install -e .
+
+RUN cd nipype/ && \
+    source activate nipypetests-3.4 && \
+    pip install -r requirements.txt && \
+    pip install -e .
+
+RUN cd nipype/ && \
+    source activate nipypetests-3.5 && \
+    pip install -r requirements.txt && \
+    pip install -e .
+
+WORKDIR /scratch
+
+# Install entrypoints
+ADD docker/circleci/run_* /usr/bin/
+RUN chmod +x /usr/bin/run_*
+
+# RUN echo 'source /etc/profile.d/nipype_tests.sh' >> /etc/bash.bashrc
+ENTRYPOINT ["/usr/bin/run_examples.sh"]
+

README.rst

@@ -18,10 +18,6 @@ NIPYPE: Neuroimaging in Python: Pipelines and Interfaces
     :target: https://pypi.python.org/pypi/nipype/
     :alt: Latest Version
 
-.. image:: https://img.shields.io/pypi/dm/nipype.svg
-    :target: https://pypi.python.org/pypi/nipype/
-    :alt: Downloads
-
 .. image:: https://img.shields.io/pypi/pyversions/nipype.svg
     :target: https://pypi.python.org/pypi/nipype/
     :alt: Supported Python versions

circle.yml

@@ -1,78 +1,46 @@
+machine:
+  services:
+    - docker
+
 dependencies:
   cache_directories:
-    - "~/.apt-cache"
-    - "~/examples/data"
-    - "~/examples/fsdata"
-    - "~/mcr"
-    - "~/spm12"
-    - "~/examples/fsl_course_data"
+    - "~/docker"
+
   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)
+    - mkdir -p "~/scratch/nose"
+
   override:
-    # Install apt packages
-    - sudo apt-get install -y fsl-core fsl-atlases fsl-mni152-templates fsl-feeds afni swig python-vtk xvfb fusefat
-    - 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 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
-    - pip install https://github.com/rtfd/readthedocs-sphinx-ext/archive/master.zip
-    - gem install fakes3
-    - 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
-machine:
-  environment:
-    FSLOUTPUTTYPE: NIFTI_GZ
+    - if [[ -e ~/docker/image.tar ]]; then docker load -i ~/docker/image.tar; fi
+    - docker build -t nipype/testbench:latest . :
+        timeout: 1600
+    - mkdir -p ~/docker; docker save nipype/testbench:latest > ~/docker/image.tar :
+        timeout: 1600
+
 test:
   override:
-    - 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"
-        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
-    - 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
+    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch --entrypoint="/usr/bin/run_builddocs.sh" nipype/testbench
+    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch nipype/testbench test_spm Linear /root/examples/ workflow3d :
         timeout: 1600
-    - source $HOME/.profile; python ~/nipype/tools/run_examples.py fmri_fsl_feeds Linear l1pipeline:
-        pwd: ../examples
-    - 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
+    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch nipype/testbench test_spm Linear /root/examples/ workflow4d :
         timeout: 1600
-    - source $HOME/.profile; python ~/nipype/tools/run_examples.py fmri_fsl_reuse Linear level1_workflow:
-        pwd: ../examples
-    - 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
+    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch nipype/testbench fmri_fsl_feeds Linear /root/examples/ l1pipeline
+    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch nipype/testbench fmri_spm_dartel Linear /root/examples/ level1 :
+        timeout: 1600
+    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch nipype/testbench fmri_spm_dartel Linear /root/examples/ l2pipeline :
+        timeout: 1600
+    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch nipype/testbench fmri_fsl_reuse Linear /root/examples/ level1_workflow
+    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch nipype/testbench fmri_spm_nested Linear /root/examples/ level1
+    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch nipype/testbench fmri_spm_nested Linear /root/examples/ l2pipeline
+    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch --entrypoint="/usr/bin/run_nosetests.sh" nipype/testbench :
+        timeout: 2600
+  post:
+    - bash docker/circleci/teardown.sh
 
 general:
   artifacts:
-    - "doc/_build/html"
-    - "~/log.txt"
-    - "nosetests.xml"
-    - "coverage.xml"
+    - "~/docs"
+    - "~/logs"
+    - "~/coverage.xml"
+    - "~/nosetests.xml"
+    - "~/builddocs.log"
+    - "~/scratch"

doc/_templates/indexsidebar.html

@@ -5,9 +5,9 @@ <h3>{{ _('Links') }}</h3>
     <li>Docs: <a href="http://nipy.org/nipype">Stable</a> · <a href="http://nipype.readthedocs.org/en/latest/">Dev</a></li>
     <li>Code: <a href="http://github.com/nipy/nipype">Github</a> · <a href="http://github.com/nipy/nipype/issues">Bugs-Requests</a></li>
     <li>Forum: <a href="http://neurostars.org/t/nipype">User</a> · <a href="http://projects.scipy.org/mailman/listinfo/nipy-devel">Developer</a></li>
-    <li><a href="http://nipy.org/software/license/index.html"><img src="https://img.shields.io/pypi/l/nipype.svg" alt="License"></a> · <a href="about.html#funding">Funding</a></li>
+    <li><a href="about.html#funding">Funding</a> · <a href="http://nipy.org/software/license/index.html"><img src="https://img.shields.io/pypi/l/nipype.svg" alt="License"></a></li>
     <li><a href="https://travis-ci.org/nipy/nipype"><img src="https://travis-ci.org/nipy/nipype.png?branch=master" alt="travis"></a> · <a href='https://coveralls.io/r/nipy/nipype'><img src='https://coveralls.io/repos/nipy/nipype/badge.png' alt='Coverage Status' /></a></li>
-    <li><a href="https://pypi.python.org/pypi/nipype/"><img src="https://img.shields.io/pypi/dm/nipype.svg" alt="Downloads"></a> · <a href='https://pypi.python.org/pypi/nipype/'><img src='https://img.shields.io/pypi/pyversions/nipype.svg' alt='Python Versions' /></a></li>
+    <a href='https://pypi.python.org/pypi/nipype/'><img src='https://img.shields.io/pypi/pyversions/nipype.svg' alt='Python Versions' /></a></li>
 </ul>
 
 {% endblock %}

doc/conf.py

@@ -82,7 +82,7 @@
 # The short X.Y version.
 version = nipype.__version__
 # The full version, including alpha/beta/rc tags.
-release = "0.11.0"
+release = "0.12.0"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/documentation.rst

@@ -9,7 +9,7 @@ Documentation
    :Release: |version|
    :Date: |today|
 
-Previous versions:  `0.11.0 <http://nipy.org/nipype/0.11.0>`_ `0.10.0 <http://nipy.org/nipype/0.10.0>`_
+Previous versions:  `0.12.0 <http://nipype.readthedocs.io/en/0.12.0/>`_ `0.11.0 <http://nipy.org/nipype/0.11.0>`_
 
 .. container:: doc2
 

doc/links_names.txt

@@ -95,7 +95,9 @@
 .. _Camino: http://web4.cs.ucl.ac.uk/research/medic/camino/pmwiki/pmwiki.php
 .. _Camino2Trackvis: http://camino-trackvis.sourceforge.net/
 .. _MRtrix: http://www.brain.org.au/software/mrtrix/index.html
+.. _MRtrix3: http://www.mrtrix.org/
 .. _MNE: https://martinos.org/mne/index.html
+.. _ANTS: http://stnava.github.io/ANTs/
 
 .. General software
 .. _gcc: http://gcc.gnu.org