Merge branch 'master' of github.com:nipy/nipype into fix/dvars

Author: chrisgorgo

.dockerignore

@@ -15,9 +15,6 @@ nipype.egg-info
 src/**/*
 src/
 
-# releasing
-Makefile
-
 # git
 .gitignore
 .git/**/*

CHANGES

@@ -3,6 +3,8 @@ Upcoming release 0.13
 
 * ENH: DVARS includes intensity normalization feature - turned on by default (https://github.com/nipy/nipype/pull/1827)
 * FIX: DVARS is correctly using sum of squares instead of standard deviation (https://github.com/nipy/nipype/pull/1827)
+* ENH: Refactoring of nipype.interfaces.utility (https://github.com/nipy/nipype/pull/1828)
+* FIX: CircleCI were failing silently. Some fixes to tests (https://github.com/nipy/nipype/pull/1833)
 * FIX: Issues in Docker image permissions, and docker documentation (https://github.com/nipy/nipype/pull/1825)
 * ENH: Revised all Dockerfiles and automated deployment to Docker Hub
        from CircleCI (https://github.com/nipy/nipype/pull/1815)

Dockerfile

@@ -31,12 +31,19 @@
 # Based on https://github.com/poldracklab/fmriprep/blob/9c92a3de9112f8ef1655b876de060a2ad336ffb0/Dockerfile
 #
 FROM ubuntu:xenial-20161213
+MAINTAINER The nipype developers https://github.com/nipy/nipype
+
+ARG DEBIAN_FRONTEND=noninteractive
+
+# Pre-cache neurodebian key
+COPY docker/files/neurodebian.gpg /root/.neurodebian.gpg
 
 # Prepare environment
-RUN apt-get update && \
+RUN apt-key add /root/.neurodebian.gpg && \
+    apt-get update && \
     apt-get install -y --no-install-recommends curl bzip2 ca-certificates xvfb && \
     curl -sSL http://neuro.debian.net/lists/xenial.us-ca.full >> /etc/apt/sources.list.d/neurodebian.sources.list && \
-    apt-key adv --recv-keys --keyserver hkp://pgp.mit.edu:80 0xA5D32F012649A5A9 && \
+    apt-key adv --refresh-keys --keyserver hkp://ha.pool.sks-keyservers.net 0xA5D32F012649A5A9 || true; \
     apt-get update
 
 # Installing freesurfer
@@ -78,6 +85,7 @@ RUN echo "cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tXG41MTcyXG4gKkN2dW
 # Installing Neurodebian packages (FSL, AFNI, git)
 RUN apt-get install -y --no-install-recommends \
                     fsl-core=5.0.9-1~nd+1+nd16.04+1 \
+                    fsl-mni152-templates=5.0.7-2 \
                     afni=16.2.07~dfsg.1-2~nd16.04+1
 
 ENV FSLDIR=/usr/share/fsl/5.0 \
@@ -171,7 +179,7 @@ RUN conda config --add channels conda-forge --add channels intel && \
     chmod +x /usr/local/miniconda/bin/* && \
     conda config --set always_yes yes --set changeps1 no && \
     conda update -q conda && \
-    chmod +x /usr/local/miniconda/bin/* && \
+    chmod +x /usr/local/miniconda/bin/*; sync && \
     conda install -y mkl=2017.0.1 \
                      numpy=1.11.2 \
                      scipy=0.18.1 \
@@ -196,7 +204,7 @@ ENV MKL_NUM_THREADS=1 \
 
 # Installing dev requirements (packages that are not in pypi)
 WORKDIR /root/
-ADD requirements.txt requirements.txt
+COPY requirements.txt requirements.txt
 RUN pip install -r requirements.txt && \
     rm -rf ~/.cache/pip
 

Makefile

@@ -32,6 +32,7 @@ trailing-spaces:
 
 clean-pyc:
 	find . -name "*.pyc" | xargs rm -f
+	find . -name "__pycache__" -type d | xargs rm -rf
 
 clean-so:
 	find . -name "*.so" | xargs rm -f

docker/Dockerfile_base

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docker/files/neurodebian.gpg

@@ -6,6 +6,4 @@ set -u
 mkdir -p /scratch/docs
 make html 2>&1 | tee /scratch/builddocs.log
 cp -r /root/src/nipype/doc/_build/html/* /scratch/docs/
-chmod 777 -R /scratch/docs
-chmod 777 /scratch/builddocs.log
 cat /scratch/builddocs.log && if grep -q "ERROR" /scratch/builddocs.log; then false; else true; fi

docker/files/run_builddocs.sh

@@ -15,5 +15,3 @@ coverage run /root/src/nipype/tools/run_examples.py $@
 arr=$@
 tmp_var=$( IFS=$' '; echo "${arr[*]}" )
 coverage xml -o "/scratch/smoketest_${tmp_var//[^A-Za-z0-9_-]/_}.xml"
-
-chmod 777 -R /scratch/logs

docker/files/run_examples.sh

@@ -36,4 +36,3 @@ fi
 
 # Copy crashfiles to scratch
 for i in $(find /root/src/nipype/ -name "crash-*" ); do cp $i /scratch/crashfiles/; done
-chmod 777 -R /scratch/*

docker/files/run_pytests.sh

@@ -7,9 +7,9 @@ set -u
 set -e
 
 mkdir -p ${CIRCLE_TEST_REPORTS}/pytest
-sudo mv ~/scratch/*.xml ${CIRCLE_TEST_REPORTS}/pytest
+mv ~/scratch/*.xml ${CIRCLE_TEST_REPORTS}/pytest
 mkdir -p ~/docs
-sudo mv ~/scratch/docs/* ~/docs/
+mv ~/scratch/docs/* ~/docs/
 mkdir -p ~/logs
-sudo mv ~/scratch/builddocs.log ~/logs/builddocs.log
-sudo mv ~/scratch/logs/* ~/logs/
+mv ~/scratch/builddocs.log ~/logs/builddocs.log
+mv ~/scratch/logs/* ~/logs/