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Merge pull request #1564 from oesteban/fix/DockerTags
[testing] Start using docker tags for circleCI
2 parents e319517 + 4489b76 commit e0d54f9

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‎.dockerignore

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.git/
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*.pyc
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*.egg-info
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__pycache__
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‎CHANGES

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11
Upcoming release 0.13
22
=====================
33

4-
* ENH: Implement missing inputs/outputs in FSL AvScale
5-
(https://github.com/nipy/nipype/pull/1563)
4+
* TST: reduce the size of docker images & use tags for images (https://github.com/nipy/nipype/pull/1564)
5+
* ENH: Implement missing inputs/outputs in FSL AvScale (https://github.com/nipy/nipype/pull/1563)
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Release 0.12.1 (August 3, 2016)

‎circle.yml

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@@ -5,33 +5,41 @@ machine:
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dependencies:
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cache_directories:
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- "~/docker"
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- "~/examples"
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- "~/.apt-cache"
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pre:
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- mkdir -p "~/scratch/nose"
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- mkdir -p "~/examples"
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# Let CircleCI cache the apt archive
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- sudo rm -rf /var/cache/apt/archives && sudo ln -s ~/.apt-cache /var/cache/apt/archives && mkdir -p ~/.apt-cache/partial
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- sudo apt-get -y update && sudo apt-get install -y wget bzip2
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override:
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- if [[ -e ~/docker/image.tar ]]; then docker load -i ~/docker/image.tar; fi
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- docker build -t nipype/testbench:latest . :
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- docker build -f docker/nipype_test_py27/Dockerfile -t nipype/nipype_test:py27 . :
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timeout: 1600
16-
- mkdir -p ~/docker; docker save nipype/testbench:latest > ~/docker/image.tar :
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- mkdir -p ~/docker; docker save nipype/nipype_test:py27 > ~/docker/image.tar :
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timeout: 1600
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- 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
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- 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
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test:
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override:
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- docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch --entrypoint="/usr/bin/run_builddocs.sh" nipype/testbench
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- docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch nipype/testbench test_spm Linear /root/examples/ workflow3d :
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- docker run -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /root/src/nipype/doc nipype/nipype_test:py27 /usr/bin/run_builddocs.sh
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- 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 test_spm Linear /root/examples/ workflow3d :
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timeout: 1600
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- docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch nipype/testbench test_spm Linear /root/examples/ workflow4d :
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- 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 test_spm Linear /root/examples/ workflow4d :
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timeout: 1600
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- docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch nipype/testbench fmri_fsl_feeds Linear /root/examples/ l1pipeline
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- docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch nipype/testbench fmri_spm_dartel Linear /root/examples/ level1 :
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- 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_feeds Linear /root/examples/ l1pipeline
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- 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_dartel Linear /root/examples/ level1 :
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timeout: 1600
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- docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch nipype/testbench fmri_spm_dartel Linear /root/examples/ l2pipeline :
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- 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_dartel Linear /root/examples/ l2pipeline :
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timeout: 1600
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- docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch nipype/testbench fmri_fsl_reuse Linear /root/examples/ level1_workflow
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- docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch nipype/testbench fmri_spm_nested Linear /root/examples/ level1
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- docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch nipype/testbench fmri_spm_nested Linear /root/examples/ l2pipeline
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- docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch --entrypoint="/usr/bin/run_nosetests.sh" nipype/testbench :
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- 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
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- 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
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- 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
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- docker run -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_nosetests.sh :
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timeout: 2600
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post:
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- bash docker/circleci/teardown.sh

‎doc/Makefile

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api:
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rm -rf api/generated
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python ../tools/build_modref_templates.py
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python -u ../tools/build_modref_templates.py
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rm -rf interfaces/generated
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python ../tools/build_interface_docs.py
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python -u ../tools/build_interface_docs.py
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@echo "Build API docs finished."
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html: clean examples2rst api htmlonly
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"results in _build/doctest/output.txt."
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gitwash-update:
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python ../tools/gitwash_dumper.py devel nipype \
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python -u ../tools/gitwash_dumper.py devel nipype \
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--repo-name=nipype \
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--github-user=nipy \
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--project-url=http://nipy.org/nipype \

‎docker/circleci/run_builddocs.sh

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#!/bin/bash
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for i in /etc/profile.d/*.sh; do
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source $i
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done
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source activate nipypetests-2.7
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set -e
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set -x
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set -u
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mkdir -p /scratch/docs
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set -o pipefail && cd /root/src/nipype/doc && make html 2>&1 | tee /scratch/builddocs.log
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make html 2>&1 | tee /scratch/builddocs.log
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cp -r /root/src/nipype/doc/_build/html/* /scratch/docs/
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chmod 777 -R /scratch/docs
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chmod 777 /scratch/builddocs.log

‎docker/circleci/run_examples.sh

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#!/bin/bash
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for i in /etc/profile.d/*.sh; do
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source $i
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done
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set -e
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set -x
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set -u
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mkdir -p /root/.nipype
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mkdir -p /scratch/logs
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echo '[logging]' > /root/.nipype/nipype.cfg
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echo 'workflow_level = DEBUG' >> /root/.nipype/nipype.cfg
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echo 'interface_level = DEBUG' >> /root/.nipype/nipype.cfg
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echo 'filemanip_level = DEBUG' >> /root/.nipype/nipype.cfg
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echo 'log_to_file = true' >> /root/.nipype/nipype.cfg
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echo 'log_directory = /scratch/logs/' >> /root/.nipype/nipype.cfg
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source activate nipypetests-2.7
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python /root/src/nipype/tools/run_examples.py $@

‎docker/circleci/run_nosetests.sh

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#!/bin/bash
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for i in /etc/profile.d/*.sh; do
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source $i
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done
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source activate nipypetests-2.7
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set -e
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set -x
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set -u
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cd /root/src/nipype
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mkdir -p /scratch/nose
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nosetests -c /root/src/nipype/.noserc --xunit-file="/scratch/nosetests.xml" --cover-xml-file="/scratch/coverage.xml"

‎docker/circleci/teardown.sh

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mkdir -p ~/docs
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sudo mv ~/scratch/docs/* ~/docs/
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mkdir -p ~/logs
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sudo mv ~/scratch/logs/* ~/logs/
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sudo mv $(pwd)/scratch/logs/* ~/logs/

‎docker/nipype_test_base/Dockerfile

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# Copyright (c) 2016, The developers of nipype
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# All rights reserved.
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#
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# Redistribution and use in source and binary forms, with or without
5+
# modification, are permitted provided that the following conditions are met:
6+
#
7+
# * Redistributions of source code must retain the above copyright notice, this
8+
# list of conditions and the following disclaimer.
9+
#
10+
# * Redistributions in binary form must reproduce the above copyright notice,
11+
# this list of conditions and the following disclaimer in the documentation
12+
# and/or other materials provided with the distribution.
13+
#
14+
# * Neither the name of crn_base nor the names of its
15+
# contributors may be used to endorse or promote products derived from
16+
# this software without specific prior written permission.
17+
#
18+
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
19+
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20+
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
21+
# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
22+
# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
23+
# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
24+
# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
25+
# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
26+
# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
27+
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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FROM neurodebian:latest
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MAINTAINER Nipype developers
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# Preparations
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RUN ln -snf /bin/bash /bin/sh
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ARG DEBIAN_FRONTEND=noninteractive
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RUN sed -i -e 's,main$,main contrib non-free,g' /etc/apt/sources.list.d/neurodebian.sources.list && \
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apt-get -y update && \
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apt-get install -y curl \
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git \
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xvfb \
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bzip2 \
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unzip \
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apt-utils \
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fusefat \
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graphviz \
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make \
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fsl-core && \
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rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && \
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echo ". /etc/fsl/fsl.sh" >> /etc/bash.bashrc
50+
51+
ENV FSLDIR=/usr/share/fsl/5.0
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ENV FSLOUTPUTTYPE=NIFTI_GZ
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ENV PATH=/usr/lib/fsl/5.0:$PATH
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ENV FSLMULTIFILEQUIT=TRUE
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ENV POSSUMDIR=/usr/share/fsl/5.0
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ENV LD_LIBRARY_PATH=/usr/lib/fsl/5.0:$LD_LIBRARY_PATH
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ENV FSLTCLSH=/usr/bin/tclsh
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ENV FSLWISH=/usr/bin/wish
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# Install Matlab: from the good old install_spm_mcr.sh of @chrisfilo
61+
WORKDIR /opt
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63+
RUN echo "destinationFolder=/opt/mcr" > mcr_options.txt && \
64+
echo "agreeToLicense=yes" >> mcr_options.txt && \
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echo "outputFile=/tmp/matlabinstall_log" >> mcr_options.txt && \
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echo "mode=silent" >> mcr_options.txt && \
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mkdir -p matlab_installer && \
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curl -sSL http://www.mathworks.com/supportfiles/downloads/R2015a/deployment_files/R2015a/installers/glnxa64/MCR_R2015a_glnxa64_installer.zip \
69+
-o matlab_installer/installer.zip && \
70+
unzip matlab_installer/installer.zip -d matlab_installer/ && \
71+
matlab_installer/install -inputFile mcr_options.txt && \
72+
rm -rf matlab_installer mcr_options.txt
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74+
ENV SPMMCRCMD "/opt/spm12/run_spm12.sh /opt/mcr/v85/ script"
75+
ENV FORCE_SPMMCR 1
76+
77+
# Install SPM
78+
RUN curl -sSL http://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/dev/spm12_r6472_Linux_R2015a.zip -o spm12.zip && \
79+
unzip spm12.zip && \
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rm -rf spm12.zip
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82+
CMD ["/bin/bash"]
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‎docker/nipype_test_py27/Dockerfile

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# Copyright (c) 2016, The developers of nipype
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# All rights reserved.
3+
#
4+
# Redistribution and use in source and binary forms, with or without
5+
# modification, are permitted provided that the following conditions are met:
6+
#
7+
# * Redistributions of source code must retain the above copyright notice, this
8+
# list of conditions and the following disclaimer.
9+
#
10+
# * Redistributions in binary form must reproduce the above copyright notice,
11+
# this list of conditions and the following disclaimer in the documentation
12+
# and/or other materials provided with the distribution.
13+
#
14+
# * Neither the name of crn_base nor the names of its
15+
# contributors may be used to endorse or promote products derived from
16+
# this software without specific prior written permission.
17+
#
18+
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
19+
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20+
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
21+
# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
22+
# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
23+
# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
24+
# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
25+
# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
26+
# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
27+
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
28+
29+
FROM nipype/nipype_test:base
30+
MAINTAINER The nipype developers https://github.com/nipy/nipype
31+
# Preparations
32+
RUN ln -snf /bin/bash /bin/sh
33+
WORKDIR /root
34+
35+
# Install miniconda
36+
RUN curl -sSLO https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh && \
37+
/bin/bash Miniconda-latest-Linux-x86_64.sh -b -p /usr/local/miniconda && \
38+
rm Miniconda-latest-Linux-x86_64.sh
39+
40+
ENV PATH /usr/local/miniconda/bin:$PATH
41+
42+
# http://bugs.python.org/issue19846
43+
# > At the moment, setting "LANG=C" on a Linux system *fundamentally breaks Python 3*, and that's not OK.
44+
ENV LANG C.UTF-8
45+
46+
# Add conda-forge channel in conda
47+
RUN conda config --add channels conda-forge && \
48+
conda install -y lockfile nipype matplotlib sphinx boto coverage
49+
50+
RUN mkdir -p /root/src/nipype
51+
COPY . /root/src/nipype
52+
53+
RUN cd /root/src/nipype && \
54+
pip install dipy && \
55+
pip install -r requirements.txt && \
56+
pip install -e .
57+
58+
59+
COPY docker/circleci/run_* /usr/bin/
60+
RUN chmod +x /usr/bin/run_*
61+
ENV SHELL /bin/bash
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63+
CMD ["/bin/bash"]

‎docker/nipype_test_py34/Dockerfile

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# Copyright (c) 2016, The developers of nipype
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# All rights reserved.
3+
#
4+
# Redistribution and use in source and binary forms, with or without
5+
# modification, are permitted provided that the following conditions are met:
6+
#
7+
# * Redistributions of source code must retain the above copyright notice, this
8+
# list of conditions and the following disclaimer.
9+
#
10+
# * Redistributions in binary form must reproduce the above copyright notice,
11+
# this list of conditions and the following disclaimer in the documentation
12+
# and/or other materials provided with the distribution.
13+
#
14+
# * Neither the name of crn_base nor the names of its
15+
# contributors may be used to endorse or promote products derived from
16+
# this software without specific prior written permission.
17+
#
18+
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
19+
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20+
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
21+
# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
22+
# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
23+
# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
24+
# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
25+
# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
26+
# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
27+
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
28+
29+
FROM nipype/nipype_test:base
30+
MAINTAINER The nipype developers https://github.com/nipy/nipype
31+
# Preparations
32+
RUN ln -snf /bin/bash /bin/sh
33+
WORKDIR /root
34+
35+
# Install miniconda
36+
RUN curl -sSLO https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
37+
/bin/bash Miniconda3-latest-Linux-x86_64.sh -b -p /usr/local/miniconda && \
38+
rm Miniconda3-latest-Linux-x86_64.sh
39+
40+
ENV PATH /usr/local/miniconda/bin:$PATH
41+
42+
# http://bugs.python.org/issue19846
43+
# > At the moment, setting "LANG=C" on a Linux system *fundamentally breaks Python 3*, and that's not OK.
44+
ENV LANG C.UTF-8
45+
46+
# Add conda-forge channel in conda
47+
RUN conda config --add channels conda-forge && \
48+
conda update -y conda && \
49+
conda update --all -y python=3.4 && \
50+
conda install -y lockfile nipype
51+
52+
RUN mkdir -p /root/src/nipype
53+
COPY . /root/src/nipype
54+
55+
RUN cd /root/src/nipype && \
56+
pip install -r requirements.txt && \
57+
pip install -e .
58+
59+
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COPY docker/circleci/run_* /usr/bin/
61+
RUN chmod +x /usr/bin/run_*
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ENV SHELL /bin/bash
63+
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CMD ["/bin/bash"]

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