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Merge pull request #1833 from oesteban/fix/TestingCircle
[BUG] Fixing CircleCI tests (several issues)
2 parents 25b46b1 + 030eae1 commit 4d8fc36

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‎CHANGES

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Upcoming release 0.13
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=====================
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* FIX: CircleCI were failing silently. Some fixes to tests (https://github.com/nipy/nipype/pull/1833)
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* FIX: Issues in Docker image permissions, and docker documentation (https://github.com/nipy/nipype/pull/1825)
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* ENH: Revised all Dockerfiles and automated deployment to Docker Hub
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from CircleCI (https://github.com/nipy/nipype/pull/1815)

‎Dockerfile

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# Based on https://github.com/poldracklab/fmriprep/blob/9c92a3de9112f8ef1655b876de060a2ad336ffb0/Dockerfile
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#
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FROM ubuntu:xenial-20161213
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MAINTAINER The nipype developers https://github.com/nipy/nipype
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ARG DEBIAN_FRONTEND=noninteractive
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# Prepare environment
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RUN apt-get update && \
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# Installing Neurodebian packages (FSL, AFNI, git)
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RUN apt-get install -y --no-install-recommends \
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fsl-core=5.0.9-1~nd+1+nd16.04+1 \
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fsl-mni152-templates=5.0.7-2 \
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afni=16.2.07~dfsg.1-2~nd16.04+1
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ENV FSLDIR=/usr/share/fsl/5.0 \
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chmod +x /usr/local/miniconda/bin/* && \
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conda config --set always_yes yes --set changeps1 no && \
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conda update -q conda && \
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chmod +x /usr/local/miniconda/bin/* && \
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chmod +x /usr/local/miniconda/bin/*; sync && \
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conda install -y mkl=2017.0.1 \
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numpy=1.11.2 \
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scipy=0.18.1 \

‎docker/Dockerfile_base

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This file was deleted.

‎docker/files/run_builddocs.sh

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mkdir -p /scratch/docs
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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
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cat /scratch/builddocs.log && if grep -q "ERROR" /scratch/builddocs.log; then false; else true; fi

‎docker/files/run_examples.sh

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arr=$@
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tmp_var=$( IFS=$' '; echo "${arr[*]}" )
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coverage xml -o "/scratch/smoketest_${tmp_var//[^A-Za-z0-9_-]/_}.xml"
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chmod 777 -R /scratch/logs

‎docker/files/run_pytests.sh

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

‎docker/files/teardown.sh

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set -e
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mkdir -p ${CIRCLE_TEST_REPORTS}/pytest
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sudo mv ~/scratch/*.xml ${CIRCLE_TEST_REPORTS}/pytest
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mv ~/scratch/*.xml ${CIRCLE_TEST_REPORTS}/pytest
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mkdir -p ~/docs
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sudo mv ~/scratch/docs/* ~/docs/
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mv ~/scratch/docs/* ~/docs/
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mkdir -p ~/logs
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sudo mv ~/scratch/builddocs.log ~/logs/builddocs.log
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sudo mv ~/scratch/logs/* ~/logs/
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mv ~/scratch/builddocs.log ~/logs/builddocs.log
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mv ~/scratch/logs/* ~/logs/

‎docker/files/tests.sh

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# They may need to be rebalanced in the future.
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case ${CIRCLE_NODE_INDEX} in
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0)
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time docker run --rm -it -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/examples/ level1
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docker run --rm -it -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/examples/ level1 && \
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docker run --rm -it -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/examples/ l2pipeline
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;;
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1)
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time docker run --rm -it -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/examples/ l2pipeline
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time docker run --rm -it -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow3d
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time docker run --rm -it -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /root/src/nipype nipype/nipype_test:py35 /usr/bin/run_pytests.sh py35
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time docker run --rm -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1
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docker run --rm -it -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow3d && \
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docker run --rm -it -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow4d && \
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docker run --rm -it -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /root/src/nipype nipype/nipype_test:py27 /usr/bin/run_pytests.sh py27 && \
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docker run --rm -it -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /root/src/nipype nipype/nipype_test:py35 /usr/bin/run_pytests.sh py35 && \
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docker run --rm -it -v $SCRATCH:/scratch -w /root/src/nipype/doc nipype/nipype_test:py35 /usr/bin/run_builddocs.sh
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;;
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2)
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time docker run --rm -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ l2pipeline
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time docker run --rm -it -v $SCRATCH:/scratch -w /root/src/nipype/doc nipype/nipype_test:py35 /usr/bin/run_builddocs.sh
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time docker run --rm -it -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /root/src/nipype nipype/nipype_test:py27 /usr/bin/run_pytests.sh py27
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time docker run --rm -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1
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docker run --rm -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1 && \
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docker run --rm -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ l2pipeline
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;;
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time docker run --rm -it -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow4d
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time docker run --rm -it -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_fsl_feeds Linear /root/examples/ l1pipeline
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time docker run --rm -it -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_fsl_reuse Linear /root/examples/ level1_workflow
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docker run --rm -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1 && \
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docker run --rm -it -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_fsl_feeds Linear /root/examples/ l1pipeline && \
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docker run --rm -it -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_fsl_reuse Linear /root/examples/ level1_workflow
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;;
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esac
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xargs -0 -I file ./codecov.io -f file -t "${CODECOV_TOKEN}" -F unittests
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find "${CIRCLE_TEST_REPORTS}/pytest" -name 'smoketests*.xml' -print0 | \
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xargs -0 -I file ./codecov.io -f file -t "${CODECOV_TOKEN}" -F smoketests
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‎nipype/testing/fixtures.py

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"""
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Pytest fixtures used in tests.
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"""
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from __future__ import print_function, division, unicode_literals, absolute_import
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import os
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import pytest
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import numpy as np
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import nibabel as nb
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from io import open
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from builtins import str
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from nipype.interfaces.fsl import Info
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from nipype.interfaces.fsl.base import FSLCommand
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def nifti_image_files(outdir, filelist, shape):
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if not isinstance(filelist, (list, tuple)):
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filelist = [filelist]
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for f in filelist:
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hdr = nb.Nifti1Header()
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hdr.set_data_shape(shape)
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img = np.random.random(shape)
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nb.save(nb.Nifti1Image(img, np.eye(4), hdr),
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os.path.join(outdir, f))
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nb.Nifti1Image(img, np.eye(4), None).to_filename(
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os.path.join(outdir, f))
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@pytest.fixture()
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cwd = os.getcwd()
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os.chdir(outdir)
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surf = 'lh.a.nii'
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nifti_image_files(outdir, filelist=surf, shape=(1,100,1))
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nifti_image_files(outdir, filelist=surf, shape=(1, 100, 1))
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def change_directory():
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os.chdir(cwd)

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