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CI: Replace test_init with DOCKER_IMAGE, -ux
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‎.circleci/config.yml

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@@ -6,6 +6,7 @@ _store_artifacts_kwds: &store_artifacts_kwds
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_test_environment: &test_environment
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WORKDIR: /home/circleci/work
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DOCKER_IMAGE: "nipype/nipype"
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_generate_dockerfiles: &generate_dockerfiles
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name: Generate Dockerfiles
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name: Run pytests (py36)
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no_output_timeout: 30m
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environment: *test_environment
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command: bash /home/circleci/nipype/.circleci/test_py3_pytest.sh
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command: bash -ux /home/circleci/nipype/.circleci/test_py3_pytest.sh
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- run:
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name: Run pytests (py27)
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no_output_timeout: 30m
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environment: *test_environment
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command: bash /home/circleci/nipype/.circleci/test_py2_pytest.sh
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command: bash -ux /home/circleci/nipype/.circleci/test_py2_pytest.sh
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- run:
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name: Build docs (py36)
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no_output_timeout: 30m
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environment: *test_environment
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command: bash /home/circleci/nipype/.circleci/test_py3_docs.sh
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command: bash -ux /home/circleci/nipype/.circleci/test_py3_docs.sh
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- run: *_run_codecov
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- store_artifacts: *store_artifacts_kwds
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name: Run FSL FEEDS pipeline (py36)
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no_output_timeout: 40m
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environment: *test_environment
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command: bash /home/circleci/nipype/.circleci/test_py3_fmri_fsl_feeds_linear_l1.sh
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command: bash -ux /home/circleci/nipype/.circleci/test_py3_fmri_fsl_feeds_linear_l1.sh
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- run:
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name: Run FSL reuse pipeline (py36)
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no_output_timeout: 40m
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environment: *test_environment
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command: bash /home/circleci/nipype/.circleci/test_py3_fmri_fsl_reuse_linear_l1.sh
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command: bash -ux /home/circleci/nipype/.circleci/test_py3_fmri_fsl_reuse_linear_l1.sh
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- run:
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name: Run SPM test workflow - 3D inputs (py36)
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no_output_timeout: 40m
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environment: *test_environment
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command: bash /home/circleci/nipype/.circleci/test_py3_fmri_spm_linear_3d.sh
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command: bash -ux /home/circleci/nipype/.circleci/test_py3_fmri_spm_linear_3d.sh
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- run:
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name: Run SPM test workflow - 4D inputs (py36)
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no_output_timeout: 40m
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environment: *test_environment
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command: bash /home/circleci/nipype/.circleci/test_py3_fmri_spm_linear_4d.sh
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command: bash -ux /home/circleci/nipype/.circleci/test_py3_fmri_spm_linear_4d.sh
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- run: *_run_codecov
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- store_artifacts: *store_artifacts_kwds
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@@ -230,12 +231,12 @@ jobs:
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name: Run SPM DARTEL Level 1 pipeline (py36)
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no_output_timeout: 1h
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environment: *test_environment
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command: bash /home/circleci/nipype/.circleci/test_py3_fmri_spm_dartel_multiproc_l1.sh
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command: bash -ux /home/circleci/nipype/.circleci/test_py3_fmri_spm_dartel_multiproc_l1.sh
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- run:
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name: Run SPM DARTEL Level 2 pipeline (py36)
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no_output_timeout: 30m
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environment: *test_environment
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command: bash /home/circleci/nipype/.circleci/test_py3_fmri_spm_dartel_multiproc_l2.sh
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command: bash -ux /home/circleci/nipype/.circleci/test_py3_fmri_spm_dartel_multiproc_l2.sh
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- run: *_run_codecov
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- store_artifacts: *store_artifacts_kwds
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@@ -259,12 +260,12 @@ jobs:
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name: Run SPM Nested Level 1 pipeline (py36)
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no_output_timeout: 1h
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environment: *test_environment
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command: bash /home/circleci/nipype/.circleci/test_py3_fmri_spm_nested_multiproc_l1.sh
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command: bash -ux /home/circleci/nipype/.circleci/test_py3_fmri_spm_nested_multiproc_l1.sh
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- run:
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name: Run SPM Nested Level 2 pipeline (py27)
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no_output_timeout: 30m
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environment: *test_environment
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command: bash /home/circleci/nipype/.circleci/test_py2_fmri_spm_nested_multiproc_l2.sh
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command: bash -ux /home/circleci/nipype/.circleci/test_py2_fmri_spm_nested_multiproc_l2.sh
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- run: *_run_codecov
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- store_artifacts: *store_artifacts_kwds
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- run:

‎.circleci/test_init.sh

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‎.circleci/test_py2_fmri_spm_nested_multiproc_l2.sh

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#!/bin/bash
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DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
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. $DIR/test_init.sh
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docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work -e NIPYPE_NUMBER_OF_CPUS=4 -e NIPYPE_RESOURCE_MONITOR=1 "${DOCKER_IMAGE}:py27" /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ l2pipeline

‎.circleci/test_py2_pytest.sh

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#!/bin/bash
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DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
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. $DIR/test_init.sh
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docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work -e CI_SKIP_TEST=1 -e NIPYPE_RESOURCE_MONITOR=1 -e FSL_COURSE_DATA="/data/examples/nipype-fsl_course_data" "${DOCKER_IMAGE}:py27" /usr/bin/run_pytests.sh

‎.circleci/test_py3_docs.sh

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#!/bin/bash
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DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
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. $DIR/test_init.sh
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docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /src/nipype/doc "${DOCKER_IMAGE}:py36" /usr/bin/run_builddocs.sh

‎.circleci/test_py3_fmri_fsl_feeds_linear_l1.sh

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#!/bin/bash
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DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
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. $DIR/test_init.sh
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docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work "${DOCKER_IMAGE}:py36" /usr/bin/run_examples.sh fmri_fsl_feeds Linear /data/examples/ l1pipeline

‎.circleci/test_py3_fmri_fsl_reuse_linear_l1.sh

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#!/bin/bash
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DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
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. $DIR/test_init.sh
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docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work "${DOCKER_IMAGE}:py36" /usr/bin/run_examples.sh fmri_fsl_reuse Linear /data/examples/ level1_workflow

‎.circleci/test_py3_fmri_spm_dartel_multiproc_l1.sh

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#!/bin/bash
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DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
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. $DIR/test_init.sh
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docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work "${DOCKER_IMAGE}:py36" /usr/bin/run_examples.sh fmri_spm_dartel MultiProc /data/examples/ level1

‎.circleci/test_py3_fmri_spm_dartel_multiproc_l2.sh

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#!/bin/bash
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DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
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. $DIR/test_init.sh
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docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work "${DOCKER_IMAGE}:py36" /usr/bin/run_examples.sh fmri_spm_dartel MultiProc /data/examples/ l2pipeline

‎.circleci/test_py3_fmri_spm_linear_3d.sh

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#!/bin/bash
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DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
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docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work "${DOCKER_IMAGE}:py36" /usr/bin/run_examples.sh test_spm Linear /data/examples/ workflow3d

‎.circleci/test_py3_fmri_spm_linear_4d.sh

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#!/bin/bash
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DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
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docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work "${DOCKER_IMAGE}:py36" /usr/bin/run_examples.sh test_spm Linear /data/examples/ workflow4d

‎.circleci/test_py3_fmri_spm_nested_multiproc_l1.sh

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#!/bin/bash
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DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
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docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work -e NIPYPE_NUMBER_OF_CPUS=4 "${DOCKER_IMAGE}:py36" /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ level1

‎.circleci/test_py3_pytest.sh

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#!/bin/bash
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DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
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. $DIR/test_init.sh
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docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work -e CI_SKIP_TEST=1 -e NIPYPE_RESOURCE_MONITOR=1 -e FSL_COURSE_DATA="/data/examples/nipype-fsl_course_data" "${DOCKER_IMAGE}:py36" /usr/bin/run_pytests.sh

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