Merge branch 'master' into enh/InterfaceLoadSettings

Author: oesteban

circle.yml

@@ -16,6 +16,7 @@ dependencies:
   override:
     - mkdir -p ~/scratch/nose ~/examples
     - if [[ ! -d ~/examples/nipype-tutorial ]]; then wget -q -O nipype-tutorial.tar.bz2 https://dl.dropbox.com/s/jzgq2nupxyz36bp/nipype-tutorial.tar.bz2 && tar xjf nipype-tutorial.tar.bz2 -C ~/examples/; fi
+    - if [[ ! -d ~/examples/nipype-fsl_course_data ]]; then wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q https://3552243d5be815c1b09152da6525cb8fe7b900a6.googledrive.com/host/0BxI12kyv2olZVUswazA3NkFvOXM/nipype-fsl_course_data.tar.gz && tar xzf nipype-fsl_course_data.tar.gz -C ~/examples/; fi
     - if [[ ! -d ~/examples/feeds ]]; then wget -q -O fsl-feeds.tar.gz https://googledrive.com/host/0BxI12kyv2olZNXBONlJKV0Y1Tm8 && tar xzf fsl-feeds.tar.gz -C ~/examples/; fi
     - if [[ -e ~/docker/image.tar ]]; then docker load -i ~/docker/image.tar; fi
     - docker build -f docker/nipype_test_py27/Dockerfile -t nipype/nipype_test:py27 . :
@@ -38,7 +39,7 @@ test:
     - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v $(pwd)/scratch:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_examples.sh fmri_fsl_reuse Linear /root/examples/ level1_workflow
     - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v $(pwd)/scratch:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_examples.sh fmri_spm_nested Linear /root/examples/ level1
     - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v $(pwd)/scratch:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_examples.sh fmri_spm_nested Linear /root/examples/ l2pipeline
-    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_nosetests.sh :
+    - docker run -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_nosetests.sh :
         timeout: 2600
   post:
     - bash docker/circleci/teardown.sh

docker/nipype_test_base/Dockerfile

@@ -31,8 +31,9 @@ MAINTAINER Nipype developers
 
 # Preparations
 RUN ln -snf /bin/bash /bin/sh
-ARG DEBIAN_FRONTEND=noninteractive
+ENV SHELL /bin/bash
 
+ARG DEBIAN_FRONTEND=noninteractive
 RUN sed -i -e 's,main$,main contrib non-free,g' /etc/apt/sources.list.d/neurodebian.sources.list && \
     apt-get -y update && \
     apt-get install -y curl \
@@ -48,14 +49,14 @@ RUN sed -i -e 's,main$,main contrib non-free,g' /etc/apt/sources.list.d/neurodeb
     rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && \
     echo ". /etc/fsl/fsl.sh" >> /etc/bash.bashrc
 
-ENV FSLDIR=/usr/share/fsl/5.0
-ENV FSLOUTPUTTYPE=NIFTI_GZ
-ENV PATH=/usr/lib/fsl/5.0:$PATH
-ENV FSLMULTIFILEQUIT=TRUE
-ENV POSSUMDIR=/usr/share/fsl/5.0
-ENV LD_LIBRARY_PATH=/usr/lib/fsl/5.0:$LD_LIBRARY_PATH
-ENV FSLTCLSH=/usr/bin/tclsh
-ENV FSLWISH=/usr/bin/wish
+ENV FSLDIR=/usr/share/fsl/5.0 \
+    FSLOUTPUTTYPE=NIFTI_GZ \
+    PATH=/usr/lib/fsl/5.0:$PATH \
+    FSLMULTIFILEQUIT=TRUE \
+    POSSUMDIR=/usr/share/fsl/5.0 \
+    LD_LIBRARY_PATH=/usr/lib/fsl/5.0:$LD_LIBRARY_PATH \
+    FSLTCLSH=/usr/bin/tclsh \
+    FSLWISH=/usr/bin/wish
 
 # Install Matlab: from the good old install_spm_mcr.sh of @chrisfilo
 WORKDIR /opt
@@ -79,5 +80,25 @@ RUN curl -sSL http://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/dev/sp
     unzip spm12.zip && \
     rm -rf spm12.zip
 
+WORKDIR /root
+# Install miniconda
+RUN curl -sSLO https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh && \
+    /bin/bash Miniconda-latest-Linux-x86_64.sh -b -p /usr/local/miniconda && \
+    rm Miniconda-latest-Linux-x86_64.sh
+
+ENV PATH /usr/local/miniconda/bin:$PATH
+
+# http://bugs.python.org/issue19846
+# > At the moment, setting "LANG=C" on a Linux system *fundamentally breaks Python 3*, and that's not OK.
+ENV LANG C.UTF-8
+
+# Add conda-forge channel in conda
+RUN conda config --add channels conda-forge && \
+    conda install -y lockfile nipype matplotlib sphinx boto coverage dipy
+
+# Install run scripts
+COPY docker/circleci/run_* /usr/bin/
+RUN chmod +x /usr/bin/run_*
+
 CMD ["/bin/bash"]
 

docker/nipype_test_py27/Dockerfile

@@ -26,38 +26,16 @@
 # 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/nipype_test:base
+FROM nipype/nipype_test:base-0.0.1
 MAINTAINER The nipype developers https://github.com/nipy/nipype
-# Preparations
-RUN ln -snf /bin/bash /bin/sh
-WORKDIR /root
 
-# Install miniconda
-RUN curl -sSLO https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh && \
-    /bin/bash Miniconda-latest-Linux-x86_64.sh -b -p /usr/local/miniconda && \
-    rm Miniconda-latest-Linux-x86_64.sh
+# Pre-check that requirements are installed
+WORKDIR /root/src/nipype
+COPY requirements.txt /root/src/nipype/requirements.txt
+RUN pip install -r requirements.txt
 
-ENV PATH /usr/local/miniconda/bin:$PATH
-
-# http://bugs.python.org/issue19846
-# > At the moment, setting "LANG=C" on a Linux system *fundamentally breaks Python 3*, and that's not OK.
-ENV LANG C.UTF-8
-
-# Add conda-forge channel in conda
-RUN conda config --add channels conda-forge && \
-    conda install -y lockfile nipype matplotlib sphinx boto coverage
-
-RUN mkdir -p /root/src/nipype
 COPY . /root/src/nipype
-
-RUN cd /root/src/nipype && \
-    pip install dipy && \
-    pip install -r requirements.txt && \
+RUN rm -r /usr/local/miniconda/lib/python2.7/site-packages/nipype* && \
     pip install -e .
 
-
-COPY docker/circleci/run_* /usr/bin/
-RUN chmod +x /usr/bin/run_*
-ENV SHELL /bin/bash
-
 CMD ["/bin/bash"]

nipype/interfaces/spm/base.py

@@ -14,13 +14,10 @@
    spm.SPMCommand().version
 """
 
+# Standard library imports
 from __future__ import print_function
 from builtins import range
 from builtins import object
-
-__docformat__ = 'restructuredtext'
-
-# Standard library imports
 import os
 from copy import deepcopy
 
@@ -38,6 +35,8 @@
 from ... import logging
 logger = logging.getLogger('interface')
 
+__docformat__ = 'restructuredtext'
+
 
 def func_is_3d(in_file):
     """Checks if input functional files are 3d."""
@@ -216,7 +215,8 @@ class SPMCommandInputSpec(BaseInterfaceInputSpec):
                         usedefault=True)
     use_mcr = traits.Bool(desc='Run m-code using SPM MCR')
     use_v8struct = traits.Bool(True, min_ver='8', usedefault=True,
-                               desc=('Generate SPM8 and higher compatible jobs')
+                               desc=('Generate SPM8 and higher '
+                                     'compatible jobs')
                                )
 
 
@@ -476,14 +476,15 @@ def _make_matlab_command(self, contents, postscript=None):
         end\n
         """
         if self.mlab.inputs.mfile:
-            if isdefined(self.inputs.use_v8struct) and self.inputs.use_v8struct:
+            if (isdefined(self.inputs.use_v8struct) and
+                    self.inputs.use_v8struct):
                 mscript += self._generate_job('jobs{1}.spm.%s.%s' %
                                               (self.jobtype, self.jobname),
                                               contents[0])
             else:
                 if self.jobname in ['st', 'smooth', 'preproc', 'preproc8',
-                                    'fmri_spec', 'fmri_est', 'factorial_design',
-                                    'defs']:
+                                    'fmri_spec', 'fmri_est',
+                                    'factorial_design', 'defs']:
                     # parentheses
                     mscript += self._generate_job('jobs{1}.%s{1}.%s(1)' %
                                                   (self.jobtype, self.jobname),