config.yml

docs_deploy: &docs
  docker:
    - image: node:8.10.0
  working_directory: /tmp/gh-pages
  steps:
    - run:
        name: Check whether this is the original repo
        command: |
          if [[ "$CIRCLE_PROJECT_USERNAME" != "nipreps" ]]; then
              echo "Not in nipreps/smriprep - skipping docs deploy."
              circleci step halt
          fi
    - add_ssh_keys:
        fingerprints:
          - "80:ec:ae:e8:92:1f:88:83:2a:e0:ee:35:39:79:85:88"
    - run:
        name: Install gh-pages tool
        command: |
          npm install -g --silent gh-pages@2.0.1
    - checkout
    - run:
        name: Set git settings
        command: |
          git config user.email "nipreps@gmail.com"
          git config user.name "nipreps-bot"
    - attach_workspace:
        at: docs/_build
    - run:
        name: Disable jekyll builds
        command: touch docs/_build/html/.nojekyll
    - run:
        name: Deploy docs to gh-pages branch
        command: gh-pages --dotfiles --message "doc(update) [skip ci]" --dist docs/_build/html

version: 2.1
orbs:
  docker: circleci/docker@1.6.0

jobs:
  build:
    machine:
      image: ubuntu-2004:202107-02
    working_directory: /tmp/src/smriprep
    environment:
      TZ: "/usr/share/zoneinfo/America/Los_Angeles"
      SCRATCH: "/scratch"
    steps:
      - restore_cache:
          keys:
            - build-v3-{{ .Branch }}-{{ epoch }}
            - build-v3-{{ .Branch }}-
            - build-v3-master-
          paths:
            - /tmp/docker
            - /tmp/images
      - docker/install-docker-credential-helper
      - run:
          name: Docker authentication
          command: |
            if [[ -n $DOCKER_PAT ]]; then
              echo "$DOCKER_PAT" | docker login -u $DOCKER_USER --password-stdin
            fi
      - run:
          name: Set up Docker registry
          command: |
            if [[ -f /tmp/images/registry.tar.gz ]]; then
              echo "Loading saved registry image"
              docker load < /tmp/images/registry.tar.gz
            else
              echo "Pulling registry image from DockerHub"
              docker pull registry:2
              mkdir -p /tmp/images
              docker save registry:2 | gzip > /tmp/images/registry.tar.gz
            fi
            docker run -d -p 5000:5000 --restart=always --name=registry \
                -v /tmp/docker:/var/lib/registry registry:2
      - run:
          name: Pull images
          command: |
            set +e
            docker pull localhost:5000/ubuntu
            success=$?
            set -e
            if [[ "$success" = "0" ]]; then
                echo "Pulling from local registry"
                docker tag localhost:5000/ubuntu ubuntu:xenial-20201030
                docker pull localhost:5000/smriprep
                docker tag localhost:5000/smriprep nipreps/smriprep:latest
                docker tag localhost:5000/smriprep nipreps/smriprep
            else
                echo "Pulling from Docker Hub"
                docker pull ubuntu:xenial-20201030
                docker tag ubuntu:xenial-20201030 localhost:5000/ubuntu
                docker push localhost:5000/ubuntu
                docker pull nipreps/smriprep:latest
            fi
      - checkout
      - run:
          name: Build Docker image
          no_output_timeout: 60m
          command: |
            export PY3=$(pyenv versions | grep '3\.' |
                         sed -e 's/.* 3\./3./' -e 's/ .*//')
            pyenv local $PY3
            # Get version, update files.
            THISVERSION=$( python3 get_version.py )
            if [[ ${THISVERSION:0:1} == "0" ]] ; then
              echo "WARNING: latest git tag could not be found"
              echo "Please, make sure you fetch all tags from upstream with"
              echo "the command ``git fetch --tags --verbose`` and push"
              echo "them to your fork with ``git push origin --tags``"
            fi
            # Build docker image
            e=1 && for i in {1..5}; do
              docker build --rm \
                --cache-from=nipreps/smriprep \
                -t nipreps/smriprep:latest \
                --build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` \
                --build-arg VCS_REF=`git rev-parse --short HEAD` \
                --build-arg VERSION="${CIRCLE_TAG:-$THISVERSION}" . \
              && e=0 && break || sleep 15
            done && [ "$e" -eq "0" ]

      - run:
          name: Docker push to local registry
          no_output_timeout: 40m
          command: |
            docker tag nipreps/smriprep:latest localhost:5000/smriprep
            docker push localhost:5000/smriprep
      - run:
          name: Docker registry garbage collection
          command: |
            docker exec -it registry /bin/registry garbage-collect --delete-untagged \
                /etc/docker/registry/config.yml
      - save_cache:
         key: build-v3-{{ .Branch }}-{{ epoch }}
         paths:
            - /tmp/docker
            - /tmp/images

      - persist_to_workspace:
          root: /tmp
          paths:
            - src/smriprep
            - .force

  get_data:
    docker:
      - image: circleci/python:3.8.5
    working_directory: /home/circleci/data
    steps:
      - restore_cache:
          keys:
            - testdata-v2-{{ .Branch }}-{{ epoch }}
            - testdata-v2-{{ .Branch }}
            - testdata-v2-
      - run:
          name: Get test data from ds000005
          command: |
            mkdir -p /tmp/data
            if [[ ! -d /tmp/data/ds005 ]]; then
              wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q \
                -O ds005_downsampled.tar.gz "https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/57f32a429ad5a101f977eb75"
              tar xvzf ds005_downsampled.tar.gz -C /tmp/data/
            else
              echo "Dataset ds000005 was cached"
            fi
      - run:
          name: Get test data from ds000054
          command: |
            if [[ ! -d /tmp/data/ds054 ]]; then
              wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q \
                -O ds054_downsampled.tar.gz "https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/57f32c22594d9001ef91bf9e"
              tar xvzf ds054_downsampled.tar.gz -C /tmp/data/
            else
              echo "Dataset ds000054 was cached"
            fi
      - run:
          name: Get FreeSurfer derivatives for ds000005
          command: |
            if [[ ! -d /tmp/ds005/freesurfer ]]; then
              mkdir -p /tmp/ds005
              wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q \
                -O ds005_derivatives_freesurfer.tar.gz "https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/58fe59eb594d900250960180"
              tar xvzf ds005_derivatives_freesurfer.tar.gz -C /tmp/ds005
            else
              echo "FreeSurfer derivatives of ds000005 were cached"
            fi
      - run:
          name: Store FreeSurfer license file
          command: |
            mkdir -p /tmp/fslicense
            cd /tmp/fslicense
            echo "cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tXG41MTcyXG4gKkN2dW12RVYzelRmZ1xuRlM1Si8yYzFhZ2c0RVxuIiA+IGxpY2Vuc2UudHh0Cg==" | base64 -d | sh
      - persist_to_workspace:
          root: /tmp
          paths:
            - fslicense
      - save_cache:
          key: testdata-v2-{{ .Branch }}-{{ epoch }}
          paths:
            - /tmp/data
            - /tmp/ds005/freesurfer
      - checkout:
          path: /tmp/src/smriprep
      - restore_cache:
          keys:
            - templateflow-v1-{{ .Branch }}-{{ epoch }}
            - templateflow-v1-{{ .Branch }}
            - templateflow-v1-
      - restore_cache:
          keys:
            - env-v1-{{ .Branch }}-{{ epoch }}
            - env-v1-{{ .Branch }}
            - env-v1-
      - run:
          name: Pull TemplateFlow down, pre-cache some templates
          command: |
            export TEMPLATEFLOW_HOME=/tmp/templateflow
            pip install -U --user --no-cache-dir "$( grep templateflow /tmp/src/smriprep/setup.cfg | xargs )"
            python -c "from templateflow import api as tfapi; \
                       tfapi.get(['MNI152Lin', 'MNI152NLin2009cAsym', 'OASIS30ANTs'], suffix='T1w'); \
                       tfapi.get(['MNI152Lin', 'MNI152NLin2009cAsym', 'OASIS30ANTs'], desc='brain', suffix='mask'); \
                       tfapi.get('OASIS30ANTs', resolution=1, desc='4', suffix='dseg'); \
                       tfapi.get(['OASIS30ANTs', 'NKI'], resolution=1, label='brain', suffix='probseg'); \
                       tfapi.get(['MNI152NLin2009cAsym', 'OASIS30ANTs', 'NKI'], resolution=1, \
                                 desc='BrainCerebellumExtraction', suffix='mask'); \
                       tfapi.get(['MNI152NLin2009cAsym', 'OASIS30ANTs', 'NKI'], resolution=1, \
                                 desc='BrainCerebellumRegistration', suffix='mask'); \
                       tfapi.get('OASIS30ANTs', resolution=1, label=['WM', 'BS'], suffix='probseg'); \
                       tfapi.get('MNI152NLin2009cAsym', resolution=2, label='WM', suffix='probseg');"
      - save_cache:
          key: templateflow-v1-{{ .Branch }}-{{ epoch }}
          paths:
            - /tmp/templateflow
      - save_cache:
          key: env-v1-{{ .Branch }}-{{ epoch }}
          paths:
            - /home/circleci/.local

  test_wrapper:
    machine:
      image: ubuntu-2004:202107-02
    steps:
      - attach_workspace:
          at: /tmp
      - restore_cache:
          keys:
            - build-v3-{{ .Branch }}-{{ epoch }}
            - build-v3-{{ .Branch }}-
            - build-v3-master-
          paths:
            - /tmp/docker
            - /tmp/images
      - docker/install-docker-credential-helper
      - run:
          name: Docker authentication
          command: |
            if [[ -n $DOCKER_PAT ]]; then
              echo "$DOCKER_PAT" | docker login -u $DOCKER_USER --password-stdin
            fi
      - run:
          name: Set up Docker registry
          command: |
            if [[ -f /tmp/images/registry.tar.gz ]]; then
              echo "Loading saved registry image"
              docker load < /tmp/images/registry.tar.gz
            else
              echo "Pulling registry image from DockerHub"
              docker pull registry:2
            fi
            docker run -d -p 5000:5000 --restart=always --name=registry \
                -v /tmp/docker:/var/lib/registry registry:2
      - run:
          name: Pull images from local registry
          command: |
            docker pull localhost:5000/smriprep
            docker tag localhost:5000/smriprep nipreps/smriprep:latest
      - checkout
      - run:
          name: Test smriprep-wrapper (Python 2)
          command: |
            export PY2=$(pyenv versions | grep '2\.' |
                         sed -e 's/.* 2\./2./' -e 's/ .*//')
            pyenv local $PY2
            echo -n "Python version: "
            python --version
            pip install --upgrade "pip<21"
            pip install --upgrade setuptools
            pip install --upgrade wrapper/
            which smriprep-docker
            smriprep-docker -i nipreps/smriprep:latest --help
            smriprep-docker -i nipreps/smriprep:latest --version
      - run:
          name: Test smriprep-wrapper (Python 3)
          command: |
            export PY3=$(pyenv versions | grep '3\.' |
                         sed -e 's/.* 3\./3./' -e 's/ .*//')
            pyenv local $PY3
            echo -n "Python version: "
            python --version
            pip install --upgrade pip setuptools
            pip install --upgrade wrapper/
            which smriprep-docker
            smriprep-docker -i nipreps/smriprep:latest --help
            smriprep-docker -i nipreps/smriprep:latest --version

  test_deploy_pypi:
    docker:
      - image: circleci/python:3.8.5
    working_directory: /tmp/src/smriprep
    steps:
      - checkout
      - run:
          name: Build sMRIPrep
          command: |
            pip install --user twine  # For use in checking distributions
            THISVERSION=$( python get_version.py )
            THISVERSION=${THISVERSION%.dirty*}
            THISVERSION=${CIRCLE_TAG:-$THISVERSION}
            virtualenv --python=python build
            source build/bin/activate
            pip install --upgrade "pip>=19.1" numpy
            echo "${CIRCLE_TAG:-$THISVERSION}" > smriprep/VERSION
            python setup.py sdist
            pip wheel --no-deps -w dist/ .
      - store_artifacts:
          path: /tmp/src/smriprep/dist
      - run:
          name: Check sdist distribution
          command: |
            THISVERSION=$( python get_version.py )
            THISVERSION=${THISVERSION%.dirty*}
            THISVERSION=${CIRCLE_TAG:-$THISVERSION}
            twine check dist/smriprep*.tar.gz
            virtualenv --python=python sdist
            source sdist/bin/activate
            pip install --upgrade "pip>=19.1" numpy
            pip install dist/smriprep*.tar.gz
            which smriprep | grep sdist\\/bin
            INSTALLED_VERSION=$(smriprep --version)
            INSTALLED_VERSION=${INSTALLED_VERSION%$'\r'}
            INSTALLED_VERSION=${INSTALLED_VERSION#*"smriprep v"}
            echo "VERSION: \"$THISVERSION\""
            echo "INSTALLED: \"$INSTALLED_VERSION\""
            test "$INSTALLED_VERSION" = "$THISVERSION"
      - run:
          name: Check wheel distribution
          command: |
            THISVERSION=$( python get_version.py )
            THISVERSION=${THISVERSION%.dirty*}
            THISVERSION=${CIRCLE_TAG:-$THISVERSION}
            twine check dist/smriprep*.whl
            virtualenv --python=python wheel
            source wheel/bin/activate
            pip install dist/smriprep*.whl
            which smriprep | grep wheel\\/bin
            INSTALLED_VERSION=$(smriprep --version)
            INSTALLED_VERSION=${INSTALLED_VERSION%$'\r'}
            INSTALLED_VERSION=${INSTALLED_VERSION#*"smriprep v"}
            echo "VERSION: \"$THISVERSION\""
            echo "INSTALLED: \"$INSTALLED_VERSION\""
            test "$INSTALLED_VERSION" = "$THISVERSION"
      - run:
          name: Build smriprep-docker
          command: |
            THISVERSION=$( python get_version.py )
            THISVERSION=${THISVERSION%.dirty*}
            cd wrapper
            virtualenv --python=python build
            source build/bin/activate
            pip install --upgrade "pip>=19.1"
            sed -i -E "s/(__version__ = )\"[A-Za-z0-9.-]+\"/\1\"${CIRCLE_TAG:-$THISVERSION}\"/" smriprep_docker.py
            python setup.py sdist
            twine check dist/smriprep*.tar.gz
            pip wheel --no-deps -w dist/ .
            twine check dist/smriprep*.whl
            pip install dist/smriprep*.whl
            set +e
            INSTALLED_VERSION=$(yes n | smriprep-docker --version)
            set -e
            INSTALLED_VERSION=${INSTALLED_VERSION%$'\r'}
            INSTALLED_VERSION=${INSTALLED_VERSION#*"smriprep wrapper "}
            INSTALLED_VERSION=$( echo ${INSTALLED_VERSION} | cut -f1 -d" ")
            echo "VERSION: \"$THISVERSION\""
            echo "INSTALLED: \"$INSTALLED_VERSION\""
            test "$INSTALLED_VERSION" = "$THISVERSION"
      - store_artifacts:
          path: /tmp/src/smriprep/wrapper/dist

  ds005:
    machine:
      image: ubuntu-2004:202107-02
    working_directory: /tmp/ds005
    environment:
      - FS_LICENSE: /tmp/fslicense/license.txt
    steps:
      - attach_workspace:
          at: /tmp
      - run:
          name: Check whether build should be skipped
          command: |
            cd /tmp/src/smriprep
            if [[ "$( git log --format=oneline -n 1 $CIRCLE_SHA1 | grep -i -E '\[skip[ _]?ds005\]' )" != "" ]]; then
              echo "Skipping ds000005 build"
              circleci step halt
            fi
      - restore_cache:
          keys:
            - build-v3-{{ .Branch }}-{{ epoch }}
            - build-v3-{{ .Branch }}-
            - build-v3-master-
          paths:
            - /tmp/docker
            - /tmp/images
      - run:
          name: Setting up test
          command: |
            mkdir -p /tmp/ds005/derivatives /tmp/ds005/work
      - run:
          name: Install codecov
          command: |
              pyenv install 3.8.5
              pyenv global 3.8.5
              python --version
              python -m pip install -U pip
              python -m pip install -U codecov
              pyenv rehash
      - docker/install-docker-credential-helper
      - run:
          name: Docker authentication
          command: |
            if [[ -n $DOCKER_PAT ]]; then
              echo "$DOCKER_PAT" | docker login -u $DOCKER_USER --password-stdin
            fi
      - run:
          name: Set up Docker registry
          command: |
            if [[ -f /tmp/images/registry.tar.gz ]]; then
              echo "Loading saved registry image"
              docker load < /tmp/images/registry.tar.gz
            else
              echo "Pulling registry image from DockerHub"
              docker pull registry:2
            fi
            docker run -d -p 5000:5000 --restart=always --name=registry \
                -v /tmp/docker:/var/lib/registry registry:2
      - run:
          name: Pull images from local registry
          command: |
            docker pull localhost:5000/smriprep
            docker tag localhost:5000/smriprep nipreps/smriprep:latest
      - restore_cache:
          keys:
            - ds005-anat-v9-{{ .Branch }}-{{ epoch }}
            - ds005-anat-v9-{{ .Branch }}
            - ds005-anat-v9-master
      - restore_cache:
          keys:
            - testdata-v2-{{ .Branch }}-{{ epoch }}
            - testdata-v2-{{ .Branch }}
            - testdata-v2-
      - restore_cache:
          keys:
            - templateflow-v1-{{ .Branch }}-{{ epoch }}
            - templateflow-v1-{{ .Branch }}
            - templateflow-v1-
      - run:
          name: Run anatomical workflow on ds005
          no_output_timeout: 2h
          command: |
            bash /tmp/src/smriprep/.circleci/ds005_run.sh --write-graph
      - run:
          name: Combine coverage
          no_output_timeout: 2h
          command: |
            # Combine coverage and convert to XML inside container because
            # the file format is sensitive to changes in environment
            docker run -it -e FMRIPREP_DEV=1 -u $(id -u):$(id -g) \
                -v /tmp/ds005:/tmp/ds005 \
                -v /tmp/src/smriprep:/src/smriprep \
                -v /tmp/templateflow:/home/smriprep/.cache/templateflow \
                -w /src/smriprep \
                -e COVERAGE_FILE=/tmp/ds005/work/.coverage \
                -e COVERAGE_RCFILE=/src/smriprep/docker/multiproc.coveragerc \
                --entrypoint=coverage \
                nipreps/smriprep:latest \
                combine /tmp/ds005/work/.coverage.*
            # Convert to XML to freeze
            docker run -it -e FMRIPREP_DEV=1 -u $(id -u) \
                -v /tmp/ds005:/tmp/ds005 \
                -v /tmp/src/smriprep:/src/smriprep \
                -v /tmp/templateflow:/home/smriprep/.cache/templateflow \
                -w /src/smriprep \
                -e COVERAGE_FILE=/tmp/ds005/work/.coverage \
                -e COVERAGE_RCFILE=/src/smriprep/docker/multiproc.coveragerc \
                --entrypoint=coverage \
                nipreps/smriprep:latest \
                xml
      - run:
          name: Combine coverage and submit
          working_directory: /tmp/src/smriprep
          command: |
              pyenv local 3.8.5
              which python
              python --version
              codecov --file coverage.xml --flags ds005 -e CIRCLE_JOB
      - run:
          name: Clean-up temporary directory of reportlets and fsdir_run_XXX nodes
          when: always
          command: |
            sudo chown $(id -un):$(id -gn) -R /tmp/ds005
            rm -rf /tmp/ds005/work/reportlets
            rm -rf /tmp/ds005/work/smriprep_wf/fsdir_run_*/
      - save_cache:
         key: ds005-anat-v9-{{ .Branch }}-{{ epoch }}
         paths:
            - /tmp/ds005/work

      - run:
          name: Checking outputs of sMRIPrep
          command: |
            mkdir -p /tmp/ds005/test
            find /tmp/ds005/derivatives -name "*" ! -path "*/figures*" -print | sed s+/tmp/ds005/derivatives/++ | sort > /tmp/ds005/test/outputs.out
            diff /tmp/src/smriprep/.circleci/ds005_outputs.txt /tmp/ds005/test/outputs.out
            exit $?
      - store_artifacts:
          path: /tmp/ds005/derivatives
      - run:
          name: Clean working directory
          when: on_success
          command: |
            rm -rf /tmp/ds005/work
      - run:
          name: Clean working directory
          when: on_fail
          command: |
            find /tmp/ds005/work \( -name "*.nii.gz" -or -name "*.nii" -or -name "*.gii" -or -name "*.h5" \) \
                -exec sh -c 'rm -f {}; touch {}' \;
      - store_artifacts:
          path: /tmp/ds005/work
      - run:
          name: Check fast track using existing derivatives
          no_output_timeout: 5m
          command: |
            bash /tmp/src/smriprep/.circleci/ds005_run.sh --fast-track
      - run:
          name: Clean working directory
          when: on_fail
          command: |
            rm -rf /tmp/ds005/work/smriprep_wf/fsdir_run_*/
            find /tmp/ds005/work \( -name "*.nii.gz" -or -name "*.nii" -or -name "*.gii" -or -name "*.h5" \) \
                -exec sh -c 'rm -f {}; touch {}' \;
      - store_artifacts:
          path: /tmp/ds005/work
          destination: fasttrack
      - store_artifacts:
          path: /tmp/ds005/derivatives
          destination: fasttrack
  ds054:
    machine:
      image: ubuntu-2004:202107-02
    working_directory: /tmp/ds054
    environment:
      - FS_LICENSE: /tmp/fslicense/license.txt
    steps:
      - attach_workspace:
          at: /tmp
      - run:
          name: Check whether build should be skipped
          command: |
            cd /tmp/src/smriprep
            if [[ "$( git log --format=oneline -n 1 $CIRCLE_SHA1 | grep -i -E '\[skip[ _]?ds054\]' )" != "" ]]; then
              echo "Skipping ds000054 build"
              circleci step halt
            fi
      - restore_cache:
          keys:
            - build-v3-{{ .Branch }}-{{ epoch }}
            - build-v3-{{ .Branch }}-
            - build-v3-master-
          paths:
            - /tmp/docker
            - /tmp/images
      - run:
          name: Setting up test
          command: |
            mkdir -p /tmp/ds054/derivatives /tmp/ds054/work
      - run:
          name: Install codecov
          command: |
              pyenv install 3.8.5
              pyenv global 3.8.5
              python --version
              python -m pip install -U pip
              python -m pip install -U codecov
              pyenv rehash
      - docker/install-docker-credential-helper
      - run:
          name: Docker authentication
          command: |
            if [[ -n $DOCKER_PAT ]]; then
              echo "$DOCKER_PAT" | docker login -u $DOCKER_USER --password-stdin
            fi
      - run:
          name: Set up Docker registry
          command: |
            if [[ -f /tmp/images/registry.tar.gz ]]; then
              echo "Loading saved registry image"
              docker load < /tmp/images/registry.tar.gz
            else
              echo "Pulling registry image from DockerHub"
              docker pull registry:2
            fi
            docker run -d -p 5000:5000 --restart=always --name=registry \
                -v /tmp/docker:/var/lib/registry registry:2
      - run:
          name: Pull images from local registry
          command: |
            docker pull localhost:5000/smriprep
            docker tag localhost:5000/smriprep nipreps/smriprep:latest
      - restore_cache:
          keys:
            - ds054-anat-v9-{{ .Branch }}-{{ epoch }}
            - ds054-anat-v9-{{ .Branch }}
            - ds054-anat-v9-master
      - restore_cache:
          keys:
            - testdata-v2-{{ .Branch }}-{{ epoch }}
            - testdata-v2-{{ .Branch }}
            - testdata-v2-
      - restore_cache:
          keys:
            - templateflow-v1-{{ .Branch }}-{{ epoch }}
            - templateflow-v1-{{ .Branch }}
            - templateflow-v1-
      - run:
          name: Run sMRIPrep on ds054 (with --fs-no-reconall)
          no_output_timeout: 2h
          command: |
            bash /tmp/src/smriprep/.circleci/ds054_run.sh --write-graph
      - run:
          name: Combine coverage
          no_output_timeout: 2h
          command: |
            # Combine coverage and convert to XML inside container because
            # the file format is sensitive to changes in environment
            docker run --rm=false -it \
                -v /tmp/ds054:/tmp/ds054 \
                -v /tmp/src/smriprep:/src/smriprep \
                -v /tmp/templateflow:/home/smriprep/.cache/templateflow \
                -w /src/smriprep \
                -e FMRIPREP_DEV=1 -u $(id -u):$(id -g) \
                -e COVERAGE_FILE=/tmp/ds054/work/.coverage \
                -e COVERAGE_RCFILE=/src/smriprep/docker/multiproc.coveragerc \
                --entrypoint=coverage \
                nipreps/smriprep:latest \
                combine /tmp/ds054/work/.coverage.*
            # Convert to XML to freeze
            docker run --rm=false -it \
                -v /tmp/ds054:/tmp/ds054 \
                -v /tmp/src/smriprep:/src/smriprep \
                -v /tmp/templateflow:/home/smriprep/.cache/templateflow \
                -w /src/smriprep \
                -e FMRIPREP_DEV=1 -u $(id -u):$(id -g) \
                -e COVERAGE_FILE=/tmp/ds054/work/.coverage \
                -e COVERAGE_RCFILE=/src/smriprep/docker/multiproc.coveragerc \
                --entrypoint=coverage \
                nipreps/smriprep:latest \
                xml
      - run:
          name: Submit coverage
          working_directory: /tmp/src/smriprep
          command: |
              pyenv local 3.8.5
              which python
              python --version
              codecov --file coverage.xml --flags ds054 -e CIRCLE_JOB
      - run:
          name: Clean-up temporary directory of reportlets
          when: always
          command: |
            sudo chown $(id -un):$(id -gn) -R /tmp/ds054
            rm -rf /tmp/ds054/work/reportlets
      - save_cache:
         key: ds054-anat-v7-{{ .Branch }}-{{ epoch }}
         paths:
            - /tmp/ds054/work
      - run:
          name: Checking outputs of sMRIPrep
          command: |
            mkdir -p /tmp/ds054/test
            find /tmp/ds054/derivatives -path */figures -prune -o -name "*" -print | sed s+/tmp/ds054/derivatives/++ | sort > /tmp/ds054/test/outputs.out
            diff /tmp/src/smriprep/.circleci/ds054_outputs.txt /tmp/ds054/test/outputs.out
            exit $?
      - run:
          name: Clean working directory
          when: on_success
          command: |
            sudo rm -rf /tmp/ds054/work
      - run:
          name: Clean working directory
          when: on_fail
          command: |
            find /tmp/ds054/work \( -name "*.nii.gz" -or -name "*.nii" -or -name "*.gii" -or -name "*.h5" \) \
                -exec sh -c 'rm -f {}; touch {}' \;
      - store_artifacts:
          path: /tmp/ds054

      - run:
          name: Check fast track using existing derivatives (with --fs-no-reconall)
          no_output_timeout: 5m
          command: |
            bash /tmp/src/smriprep/.circleci/ds054_run.sh --fast-track
      - store_artifacts:
          path: /tmp/ds054/work
          destination: fasttrack-work
      - store_artifacts:
          path: /tmp/ds054/derivatives
          destination: fasttrack-derivatives

  build_docs:
    docker:
      - image: circleci/python:3.8.5
    working_directory: /tmp/gh-pages
    environment:
      - FSLOUTPUTTYPE: NIFTI
      - SUBJECTS_DIR: /tmp/subjects
    steps:
      - checkout
      - run:
          name: Install Graphviz
          command: sudo apt update && sudo apt -y install graphviz
      - run:
          name: Update pip
          command: pip install --upgrade pip
      - run:
          name: Install deps
          command: pip install -r docs/requirements.txt
      - run:
          name: Build only this commit
          no_output_timeout: 30m
          command: make -C docs NO_ET=1 SPHINXOPTS="-W" BUILDDIR="_build/no_version_html" html
      - store_artifacts:
          path: ./docs/_build/no_version_html/html
          destination: noversion
      - run:
          name: Stop or generate versioned docs?
          command: |
            set +e
            force_versioned="$( git log --format=oneline -n 1 $CIRCLE_SHA1 | grep -i -E '\[docs?[ _]?versions?\]' )"
            set -e
            if [[ "x${CIRCLE_TAG}" = "x" && "${CIRCLE_BRANCH}" != "master" && "x${force_versioned}" = "x" ]]; then
              echo "Not a tag or master branch - skipping versioned docs."
              circleci step halt
            fi
      - run:
          name: Clean-up unversioned docs
          command: make -C docs clean
      - restore_cache:
          keys:
            - docs-v2-{{ .Branch }}-{{ .Revision }}
            - docs-v2-{{ .Branch }}-
            - docs-v2-master
            - docs-v2-
          paths:
            - ./docs/_build
      - run:
          name: Generate Versioned Docs
          command: make -f ./docs/Makefile NO_ET=1 versioned CURBRANCH=${CIRCLE_TAG:-$CIRCLE_BRANCH}
      - save_cache:
          key: docs-v2-{{ .Branch }}-{{ .Revision }}
          paths:
            - ./docs/_build
      - persist_to_workspace:
          root: docs/_build
          paths: html
      - store_artifacts:
          path: ./docs/_build/html
          destination: versioned

  deploy_pypi:
    docker:
      - image: circleci/python:3.8.5
    working_directory: /tmp/src/smriprep
    steps:
      - checkout
      - run:
          name: Build sMRIPrep
          command: |
            THISVERSION=$( python get_version.py )
            virtualenv --python=python build
            source build/bin/activate
            pip install --upgrade "pip>=19.1"
            echo "${CIRCLE_TAG:-$THISVERSION}" > smriprep/VERSION
            python setup.py sdist
            pip wheel --no-deps -w dist/ .
      - run:
          name: Build smriprep-docker
          command: |
            THISVERSION=$( python get_version.py )
            cd wrapper
            virtualenv --python=python build
            source build/bin/activate
            pip install --upgrade "pip>=19.1"
            sed -i -E "s/(__version__ = )\"[A-Za-z0-9.-]+\"/\1\"${CIRCLE_TAG:-$THISVERSION}\"/" smriprep_docker.py
            python setup.py sdist
            pip wheel --no-deps -w dist/ .
      - run:
          name: Upload packages to PyPI
          command: |
            pip install --user twine
            twine upload dist/smriprep* wrapper/dist/smriprep*

  deploy_docker:
    machine:
      image: ubuntu-2004:202107-02
    working_directory: /tmp/src/smriprep
    steps:
      - restore_cache:
          keys:
            - build-v3-{{ .Branch }}-{{ epoch }}
            - build-v3-{{ .Branch }}-
            - build-v3-master-
          paths:
            - /tmp/docker
      - run:
          name: Set-up a Docker registry
          command: |
            docker run -d -p 5000:5000 --restart=always --name=registry \
                -v /tmp/docker:/var/lib/registry registry:2
      - run:
          name: Pull images from local registry
          command: |
            docker pull localhost:5000/smriprep
            docker tag localhost:5000/smriprep nipreps/smriprep:latest
      - run:
          name: Deploy to Docker Hub
          no_output_timeout: 40m
          command: |
            if [[ -n "$DOCKER_PAT" ]]; then
              echo "$DOCKER_PAT" | docker login -u $DOCKER_USER --password-stdin
              docker tag nipreps/smriprep nipreps/smriprep:unstable
              docker push nipreps/smriprep:unstable
              if [[ -n "$CIRCLE_TAG" ]]; then
                docker push nipreps/smriprep:latest
                docker tag nipreps/smriprep nipreps/smriprep:$CIRCLE_TAG
                docker push nipreps/smriprep:$CIRCLE_TAG
              fi
            fi

  deploy_docs_tag:
    <<: *docs

  deploy_docs_master:
    <<: *docs

workflows:
  version: 2
  build_test_deploy:
    jobs:
      - build:
          filters:
            branches:
              ignore:
                - /docs?\/.*/
            tags:
              only: /.*/

      - get_data:
          filters:
            branches:
              ignore:
                - /docs?\/.*/
                - /tests?\/.*/
            tags:
              only: /.*/

      - test_deploy_pypi:
          filters:
            branches:
              only:
                - /rel\/.*/
                - /maint\/.*/
            tags:
              only: /.*/

      - test_wrapper:
          requires:
            - build
          filters:
            branches:
              ignore:
                - /docs?\/.*/
                - /ds005\/.*/
                - /ds054\/.*/
            tags:
              only: /.*/

      - build_docs:
          filters:
            branches:
              ignore:
                - /tests?\/.*/
                - /ds005\/.*/
                - /ds054\/.*/
            tags:
              only: /.*/

      - ds005:
          requires:
            - get_data
            - build
          filters:
            branches:
              ignore:
                - /docs?\/.*/
                - /tests?\/.*/
                - /ds054\/.*/
            tags:
              only: /.*/

      - ds054:
          requires:
            - get_data
            - build
          filters:
            branches:
              ignore:
                - /docs?\/.*/
                - /tests?\/.*/
                - /ds005\/.*/
            tags:
              only: /.*/


      - deploy_docs_master:
          requires:
            - build_docs
            - ds005
            - ds054
            - test_wrapper
          filters:
            branches:
              only: /master/
            tags:
              ignore: /.*/

      - deploy_docs_tag:
          requires:
            - build_docs
            - ds005
            - ds054
            - test_deploy_pypi
            - test_wrapper
          filters:
            branches:
              ignore: /.*/
            tags:
              only: /.*/

      - deploy_pypi:
          requires:
            - deploy_docs_tag
          filters:
            branches:
              ignore: /.*/
            tags:
              only: /.*/

      - deploy_docker:
          requires:
            - build
            - ds005
            - ds054
          filters:
            branches:
              only: master
            tags:
              only: /.*/