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jakubk
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update circleci config.yml
- install dependency codecov - update nipype/info.py if CIRCLE_TAG is set - retry docker image builds - download test data - fix workdir permission denied issue - save all docker images to single tarball - pipe dockerhub password to `docker login` - push all docker images to docker hub on success
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‎.circleci/config.yml‎

Lines changed: 99 additions & 58 deletions
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@@ -1,49 +1,34 @@
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# Examples:
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# https://github.com/circleci/frontend/blob/master/.circleci/config.yml
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#
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# Questions
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# ---------
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# 1. Regarding the cache: what if the base Dockerfile is reverted to a previous
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# version? The cache for that Dockerfile will exist, so it will pull the
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# image, which is incorrect. Include a note in generate_dockerfiles.sh to
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# increase the version of the cache.
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version: 2
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jobs:
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compare_base_dockerfiles:
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docker:
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- image: docker:17.06.2-ce-git # shell is /bin/ash (bash not available)
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- image: docker:17.09.0-ce-git
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steps:
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- checkout:
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path: /home/circleci/nipype
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- run:
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name: Prune base Dockerfile in preparation for cache check
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working_directory: /home/circleci/nipype/docker
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command: |
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mkdir -p /tmp/docker
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# Remove empty lines, comments, and the timestamp from the base
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# Dockerfile. Use the sha256 sum of this pruned Dockerfile as the
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# cache key.
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sed -e '/\s*#.*$/d' \
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-e '/^\s*$/d' \
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-e '/generation_timestamp/d' \
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/home/circleci/nipype/docker/Dockerfile.base \
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> /tmp/docker/Dockerfile.base-pruned
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# Use the sha256 sum of the pruned Dockerfile as the cache key.
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ash prune_dockerfile.sh Dockerfile.base > /tmp/docker/Dockerfile.base-pruned
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- restore_cache:
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key: dftest-v4-master-{{ checksum "/tmp/docker/Dockerfile.base-pruned" }}
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# TODO: change this to 'master' after we are sure this works.
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key: dftest-v5-enh/circleci-neurodocker-{{ checksum "/tmp/docker/Dockerfile.base-pruned" }}
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- run:
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name: Determine how to get base image
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command: |
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GET_BASE="/tmp/docker/get_base_image.sh"
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# This directory comes from the cache.
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if [ -d /cache/base-dockerfile ]; then
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echo 'echo Pulling base image ...' > "$GET_BASE"
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echo 'docker pull kaczmarj/nipype:base' >> "$GET_BASE"
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echo "echo Pulling base image ..." > "$GET_BASE"
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echo "docker pull kaczmarj/nipype:base" >> "$GET_BASE"
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else
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echo 'echo Building base image ...' > "$GET_BASE"
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echo 'docker build -t kaczmarj/nipype:base - < /home/circleci/nipype/docker/Dockerfile.base' >> "$GET_BASE"
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echo "echo Building base image ..." > "$GET_BASE"
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echo "docker build -t kaczmarj/nipype:base - < /home/circleci/nipype/docker/Dockerfile.base" >> "$GET_BASE"
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fi
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- persist_to_workspace:
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root: /tmp
@@ -52,8 +37,7 @@ jobs:
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build_and_test:
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parallelism: 1
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# Ideally, we could test inside the main docker image.
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parallelism: 4
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machine:
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# Ubuntu 14.04 with Docker 17.03.0-ce
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image: circleci/classic:201703-01
@@ -62,48 +46,92 @@ jobs:
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path: /home/circleci/nipype
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- attach_workspace:
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at: /tmp
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- run:
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name: Get test dependencies
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command: |
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pip install --no-cache-dir codecov
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- run:
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name: Modify Nipype version if necessary
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working_directory: /home/circleci/nipype
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command: |
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if [ "$CIRCLE_TAG" != "" ]; then
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sed -i -E "s/(__version__ = )'[A-Za-z0-9.-]+'/\1'$CIRCLE_TAG'/" nipype/info.py
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fi
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- run:
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name: Get base image (pull or build)
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no_output_timeout: 60m
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# TODO: remove `docker pull` once once caching works.
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command: |
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bash /tmp/docker/get_base_image.sh
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# bash /tmp/docker/get_base_image.sh
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docker pull kaczmarj/nipype:base
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- run:
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name: Build main image (latest & py36)
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name: Build main image (py36)
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no_output_timeout: 60m
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working_directory: /home/circleci/nipype
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command: |
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cd /home/circleci/nipype
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docker build --rm=false \
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--tag kaczmarj/nipype:latest \
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--tag kaczmarj/nipype:py36 \
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--build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` \
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--build-arg VCS_REF=`git rev-parse --short HEAD` \
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--build-arg VERSION=$CIRCLE_TAG .
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e=1 && for i in {1..5}; do
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docker build \
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--rm=false \
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--tag kaczmarj/nipype:latest \
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--tag kaczmarj/nipype:py36 \
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--build-arg BUILD_DATE="$(date -u +"%Y-%m-%dT%H:%M:%SZ")" \
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--build-arg VCS_REF="$(git rev-parse --short HEAD)" \
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--build-arg VERSION="${CIRCLE_TAG}" /home/circleci/nipype \
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&& e=0 && break || sleep 15
81+
done && [ "$e" -eq "0" ]
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- run:
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name: Build main image (py27)
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no_output_timeout: 60m
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working_directory: /home/circleci/nipype
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command: |
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cd /home/circleci/nipype
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e=1 && for i in {1..5}; do
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docker build \
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--rm=false \
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--tag kaczmarj/nipype:py27 \
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--build-arg PYTHON_VERSION_MAJOR=2 \
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--build-arg PYTHON_VERSION_MINOR=7 \
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--build-arg BUILD_DATE="$(date -u +"%Y-%m-%dT%H:%M:%SZ")" \
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--build-arg VCS_REF="$(git rev-parse --short HEAD)" \
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--build-arg VERSION="${CIRCLE_TAG}-py27" /home/circleci/nipype \
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&& e=0 && break || sleep 15
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done && [ "$e" -eq "0" ]
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- run:
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name: Download test data
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no_output_timeout: 20m
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working_directory: /home/circleci/examples
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environment:
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OSF_NIPYPE_URL: "https://files.osf.io/v1/resources/nefdp/providers/osfstorage"
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command: |
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export DATA_NIPYPE_TUTORIAL_URL="${OSF_NIPYPE_URL}/57f4739cb83f6901ed94bf21"
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curl -sSL --retry 5 --connect-timeout 15 "$DATA_NIPYPE_TUTORIAL_URL" | tar xj
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export DATA_NIPYPE_FSL_COURSE="${OSF_NIPYPE_URL}/57f472cf9ad5a101f977ecfe"
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curl -sSL --retry 5 --connect-timeout 15 "$DATA_NIPYPE_FSL_COURSE" | tar xz
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docker build --rm=false \
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--tag kaczmarj/nipype:py27 \
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--build-arg PYTHON_VERSION_MAJOR=2 \
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--build-arg PYTHON_VERSION_MINOR=7 \
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--build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` \
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--build-arg VCS_REF=`git rev-parse --short HEAD` \
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--build-arg VERSION=$CIRCLE_TAG-py27 /home/circleci/nipype
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export DATA_NIPYPE_FSL_FEEDS="${OSF_NIPYPE_URL}/57f473066c613b01f113e7af"
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curl -sSL --retry 5 --connect-timeout 15 "$DATA_NIPYPE_FSL_FEEDS" | tar xz
95113
- run:
96114
name: Run tests
115+
no_output_timeout: 4h
116+
environment:
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WORKDIR: /home/circleci/work
97118
command: |
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echo "This is node $CIRCLE_NODE_INDEX"
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echo "No tests to run yet."
119+
mkdir -p "$WORKDIR"
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chmod -R 777 "$WORKDIR"
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bash /home/circleci/nipype/.circleci/tests.sh
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- store_artifacts:
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path: /home/circleci/work/tests
100124
- run:
101125
name: Save Docker images to workspace
102126
no_output_timeout: 60m
103127
command: |
104128
if [ "$CIRCLE_NODE_INDEX" -eq "0" ]; then
105129
echo "Saving Docker images to tar.gz files ..."
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docker save kaczmarj/nipype:latest kaczmarj/nipype:py36 | gzip > /tmp/docker/nipype-latest-py36.tar.gz
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docker save kaczmarj/nipype:base \
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kaczmarj/nipype:latest \
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kaczmarj/nipype:py36 \
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kaczmarj/nipype:py27 > /tmp/docker/nipype-base-latest-py36-py27.tar
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echo "$(du -h /tmp/docker/nipype-base-latest-py36-py27.tar)"
107135
fi
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- persist_to_workspace:
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root: /tmp
@@ -113,7 +141,7 @@ jobs:
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deploy:
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docker:
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- image: docker:17.06.2-ce-git
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- image: docker:17.09.0-ce-git
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steps:
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- checkout
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- setup_remote_docker
@@ -123,18 +151,27 @@ jobs:
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name: Load saved Docker images.
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no_output_timeout: 60m
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command: |
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docker load < /tmp/docker/nipype-latest-py36.tar.gz
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docker load < /tmp/docker/nipype-base-latest-py36-py27.tar
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- run:
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name: Push to DockerHub
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no_output_timeout: 60m
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no_output_timeout: 120m
130158
command: |
131-
if [ "${CIRCLE_BRANCH}" == "enh/circleci-neurodocker" ]; then
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docker login -u $DOCKER_USER -p $DOCKER_PASS
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docker push kaczmarj/nipype:latest
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docker push kaczmarj/nipype:py36
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fi
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# TODO: write pruned Dockerfile to cache here. Make a shell script that will
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# prune Dockerfiles
159+
echo "$DOCKER_PASS" | docker login -u "$DOCKER_USER" --password-stdin
160+
docker push kaczmarj/nipype:base
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docker push kaczmarj/nipype:latest
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docker push kaczmarj/nipype:py36
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docker push kaczmarj/nipype:py27
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- run:
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name: Prune base Dockerfile to update cache
166+
command: |
167+
cd /home/circleci/nipype/docker
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# Use the sha256 sum of the pruned Dockerfile as the cache key.
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ash prune_dockerfile.sh Dockerfile.base > /tmp/docker/Dockerfile.base-pruned
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- save_cache:
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paths:
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- /tmp/docker/Dockerfile.base-pruned
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key: dftest-v5-{{ .Branch }}-{{ checksum "/tmp/docker/Dockerfile.base-pruned" }}
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workflows:
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version: 2
@@ -145,5 +182,9 @@ workflows:
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requires:
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- compare_base_dockerfiles
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- deploy:
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filters:
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branches:
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# TODO: change this to master after we are sure this works.
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only: enh/circleci-neurodocker
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requires:
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- build_and_test

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