Merge pull request #15 from BIDS-Apps/circleci2

Circleci2

.circleci/config.yml

@@ -0,0 +1,342 @@
+version: 2
+jobs:
+  get_data:
+    machine:
+      image: circleci/classic:201711-01
+    working_directory: /tmp/data
+    steps:
+      - restore_cache:
+          keys:
+            - data-v3-{{ .Revision }}
+            - data-v3-
+      - run:
+          name: Get ds114_test1
+          command: |
+            mkdir -p /tmp/data
+            if [[ ! -d /tmp/data/ds114_test1 ]]; then
+              wget -c -O ~/ds114_test1.tar \
+              "https://files.osf.io/v1/resources/9q7dv/providers/osfstorage/57e54a326c613b01d7d3ed90" && \
+              tar xf ~/ds114_test1.tar -C /tmp/data && \
+              rm ~/ds114_test1.tar;
+            else
+              echo "ds114_test1 was cached"
+            fi
+      - run:
+          name: Get ds114_test2
+          command: |
+            mkdir -p /tmp/data
+            if [[ ! -d /tmp/data/ds114_test2 ]]; then
+              wget -c -O ~/ds114_test2.tar \
+              "https://files.osf.io/v1/resources/9q7dv/providers/osfstorage/57e549f9b83f6901d457d162" && \
+              tar xf ~/ds114_test2.tar -C /tmp/data && \
+              rm ~/ds114_test2.tar;
+            else
+              echo "ds114_test2 was cached"
+            fi
+      - run:
+          name: Get ds114_test1_freesurfer
+          command: |
+            mkdir -p /tmp/data
+            if [[ ! -d /tmp/data/ds114_test1_freesurfer ]]; then
+              wget -c -O ~/ds114_test1_freesurfer.tar \
+              "https://files.osf.io/v1/resources/9q7dv/providers/osfstorage/5882adf3b83f6901f564da49" && \
+              tar xf ~/ds114_test1_freesurfer.tar -C /tmp/data && \
+              rm ~/ds114_test1_freesurfer.tar;
+            else
+              echo "ds114_test1_freesurfer was cached"
+            fi
+      - run:
+          name: Get ds114_test2_freesurfer
+          command: |
+            mkdir -p /tmp/data
+            if [[ ! -d /tmp/data/ds114_test2_freesurfer ]]; then
+              wget -c -O ~/ds114_test2_freesurfer.tar \
+              "https://files.osf.io/v1/resources/9q7dv/providers/osfstorage/5882b0e3b83f6901fb64da18" && \
+              tar xf ~/ds114_test2_freesurfer.tar -C /tmp/data && \
+              rm ~/ds114_test2_freesurfer.tar;
+            else
+              echo "ds114_test2_freesurfer was cached"
+            fi
+      - save_cache:
+         key: data-v3-{{ .Revision }}-{{ epoch }}
+         paths:
+            - /tmp/data
+
+  build:
+    docker:
+      - image: docker:18.01.0-ce-git
+    steps:
+      - checkout
+      - run:
+          name: Install parallel gzip
+          command: |
+            apk add --no-cache pigz
+      - restore_cache:
+          keys:
+            - docker-v2-{{ .Branch }}-{{ .Revision }}
+            - docker-v2-{{ .Branch }}-
+            - docker-v2-master-
+            - docker-v2-
+          paths:
+            - /tmp/cache/docker.tar.gz
+      - setup_remote_docker
+      - run:
+          name: Load Docker image layer cache
+          no_output_timeout: 30m
+          command: |
+            docker info
+            set +o pipefail
+            if [ -f /tmp/cache/docker.tar.gz ]; then
+              pigz -d --stdout /tmp/cache/docker.tar.gz | docker load
+            else
+              echo "No docker cache found"
+            fi
+            docker images
+      - run:
+          name: get version
+          command: |
+            git describe --tags --always > version
+            cat version
+      - run:
+          name: Build Docker image
+          no_output_timeout: 60m
+          command: |
+            docker images
+            set +o pipefail
+            docker build --cache-from=bids/${CIRCLE_PROJECT_REPONAME} \
+            -t bids/${CIRCLE_PROJECT_REPONAME}:latest .
+            docker images
+      - run:
+          name: Docker save
+          no_output_timeout: 40m
+          command: |
+            mkdir -p /tmp/cache
+            set +o pipefail
+            docker save bids/${CIRCLE_PROJECT_REPONAME}:latest \
+              | pigz -2 -p 3 > /tmp/cache/docker.tar.gz
+      - save_cache:
+           key: docker-v2-{{ .Branch }}-{{ epoch }}
+           paths:
+             - /tmp/cache/docker.tar.gz
+      # Usage and version
+      - run:
+          name: Usage BIDS
+          command: docker run -ti --rm bids/${CIRCLE_PROJECT_REPONAME}:latest -h
+      - run:
+          name: Usage files
+          command: docker run --rm -ti --entrypoint=run_brain_age_files.py bids/${CIRCLE_PROJECT_REPONAME}:latest -h
+      - run:
+          name: Version BIDS
+          command: docker run -ti --rm bids/${CIRCLE_PROJECT_REPONAME}:latest -v
+      - run:
+          name: Version files
+          command: docker run --rm -ti --entrypoint=run_brain_age_files.py bids/${CIRCLE_PROJECT_REPONAME}:latest -v
+      - run:
+          name: Python packages
+          command: docker run --rm -ti --entrypoint=/bin/bash bids/${CIRCLE_PROJECT_REPONAME}:latest -c "pip freeze"
+
+  test:
+    machine:
+      image: circleci/classic:201711-01
+    working_directory: /tmp/data
+    environment:
+      - DATADIR: '/tmp/data'
+      - OUTDIR: '/tmp/outputs'
+    steps:
+      - run:
+          name: Install parallel gzip
+          command: |
+            sudo apt-get update && sudo apt-get install -y pigz
+      - restore_cache:
+          keys:
+            - docker-v2-{{ .Branch }}-{{ .Revision }}
+            - docker-v2-{{ .Branch }}-
+            - docker-v2-master-
+            - docker-v2-
+          paths:
+            - /tmp/cache/docker.tar.gz
+      - restore_cache:
+          keys:
+            - data-v3-{{ .Revision }}
+            - data-v3-
+
+      # Load Docker
+      - run:
+          name: Load Docker
+          no_output_timeout: 30m
+          command: |
+            docker info
+            set +o pipefail
+            pigz -d --stdout /tmp/cache/docker.tar.gz | docker load
+            docker images
+
+      - run:
+          name: make output directory
+          command: mkdir -p ${OUTDIR}
+
+      # Test 1: ds114_test1
+      - run:
+          name: Test 1 ds114_test1 - 1
+          command: |
+            docker run --rm -ti -v ${DATADIR}/ds114_test1:/data/in \
+            -v ${DATADIR}/ds114_test1_freesurfer:/data/fs \
+            -v ${OUTDIR}/ds114_test1:/data/out \
+            bids/${CIRCLE_PROJECT_REPONAME}:latest \
+            /data/in /data/out participant --freesurfer_dir /data/fs \
+            --license_key="~/test.key"
+      - run:
+          name: Test 1 ds114_test1 - 2
+          command: |
+            docker run --rm -ti -v ${DATADIR}/ds114_test1:/data/in \
+            -v ${DATADIR}/ds114_test1_freesurfer:/data/fs \
+            -v ${OUTDIR}/ds114_test1:/data/out \
+            bids/${CIRCLE_PROJECT_REPONAME}:latest \
+            /data/in /data/out group --freesurfer_dir /data/fs \
+            --license_key="~/test.key"
+      - run:
+          name: Test 1 ds114_test1 - 3
+          command: |
+            cat ${OUTDIR}/ds114_test1/baracus/00_group/group_predicted_age.tsv
+
+
+      # Test2 : models
+      - run:
+          name: Test 2 models - 1
+          command: |
+            docker run --rm -ti -v ${DATADIR}/ds114_test1:/data/in \
+            -v ${DATADIR}/ds114_test1_freesurfer:/data/fs \
+            -v ${OUTDIR}/ds114_test1_models:/data/out \
+            bids/${CIRCLE_PROJECT_REPONAME}:latest \
+            /data/in /data/out participant --freesurfer_dir /data/fs \
+            --license_key="~/test.key" \
+            --models Liem2016__OCI_norm Liem2016__full_2samp_training
+      - run:
+          name: Test 2 models - 2
+          command: |
+            docker run --rm -ti -v ${DATADIR}/ds114_test1:/data/in \
+            -v ${DATADIR}/ds114_test1_freesurfer:/data/fs \
+            -v ${OUTDIR}/ds114_test1_models:/data/out \
+            bids/${CIRCLE_PROJECT_REPONAME}:latest \
+            /data/in /data/out group --freesurfer_dir /data/fs \
+            --license_key="~/test.key"
+      - run:
+          name: Test 2 models - 3
+          command: |
+            cat ${OUTDIR}/ds114_test1_models/baracus/00_group/group_predicted_age.tsv
+
+      # Test3: file mode
+      - run:
+          name: Test 3 file mode - 1
+          command: |
+            docker run --rm -ti \
+            -v ${OUTDIR}/ds114_test1/baracus/sub-01/data/:/data/in \
+            -v ${OUTDIR}/ds114_test1_file_mode:/data/out \
+            --entrypoint=run_brain_age_files.py \
+            bids/${CIRCLE_PROJECT_REPONAME}:latest \
+            /data/out \
+            --lh_thickness_file /data/in/lh.thickness.mgh \
+            --rh_thickness_file /data/in/rh.thickness.mgh \
+            --lh_area_file /data/in/lh.area.mgh \
+            --rh_area_file /data/in/rh.area.mgh \
+            --aseg_file /data/in/aseg --participant_label sub-01
+      - run:
+          name: Test 3 file mode - 2
+          command: |
+            cat ${OUTDIR}/ds114_test1_file_mode/sub-01/sub-01_predicted_age.tsv
+
+
+      # Test 4: ds114_test2
+      - run:
+          name: Test 1 ds114_test2 - 1
+          command: |
+            docker run --rm -ti -v ${DATADIR}/ds114_test2:/data/in \
+            -v ${DATADIR}/ds114_test2_freesurfer:/data/fs \
+            -v ${OUTDIR}/ds114_test2:/data/out \
+            bids/${CIRCLE_PROJECT_REPONAME}:latest \
+            /data/in /data/out participant --freesurfer_dir /data/fs \
+            --license_key="~/test.key"
+      - run:
+          name: Test 1 ds114_test2 - 2
+          command: |
+            docker run --rm -ti -v ${DATADIR}/ds114_test2:/data/in \
+            -v ${DATADIR}/ds114_test2_freesurfer:/data/fs \
+            -v ${OUTDIR}/ds114_test2:/data/out \
+            bids/${CIRCLE_PROJECT_REPONAME}:latest \
+            /data/in /data/out group --freesurfer_dir /data/fs \
+            --license_key="~/test.key"
+      - run:
+          name: Test 1 ds114_test2 - 3
+          command: |
+            cat ${OUTDIR}/ds114_test2/baracus/00_group/group_predicted_age.tsv
+
+      - store_artifacts:
+          path: /tmp/outputs/
+
+  deploy:
+    machine:
+      image: circleci/classic:201711-01
+    steps:
+      - run:
+          name: Install parallel gzip
+          command: |
+            sudo apt-get update && sudo apt-get install -y pigz
+      - restore_cache:
+          keys:
+            - docker-v2-{{ .Branch }}-{{ .Revision }}
+            - docker-v2-{{ .Branch }}-
+            - docker-v2-master-
+            - docker-v2-
+          paths:
+            - /tmp/cache/docker.tar.gz
+
+      # Load Docker
+      - run:
+          name: Load Docker
+          no_output_timeout: 30m
+          command: |
+            docker info
+            set +o pipefail
+            pigz -d --stdout /tmp/cache/docker.tar.gz | docker load
+            docker images
+      - run:
+          name: Deploy to Docker Hub
+          no_output_timeout: 40m
+          command: |
+            if [[ -n "$DOCKER_PASS" ]]; then
+              docker login -u $DOCKER_USER -p $DOCKER_PASS
+              docker tag bids/${CIRCLE_PROJECT_REPONAME} bids/${CIRCLE_PROJECT_REPONAME}:unstable
+              docker push bids/${CIRCLE_PROJECT_REPONAME}:unstable
+              if [[ -n "$CIRCLE_TAG" ]]; then
+                docker push bids/${CIRCLE_PROJECT_REPONAME}:latest
+                docker tag bids/${CIRCLE_PROJECT_REPONAME} bids/${CIRCLE_PROJECT_REPONAME}:$CIRCLE_TAG
+                docker push bids/${CIRCLE_PROJECT_REPONAME}:$CIRCLE_TAG
+              fi
+            fi
+
+workflows:
+  version: 2
+  build_test_deploy:
+    jobs:
+      - get_data:
+          filters:
+            tags:
+              only: /.*/
+      - build:
+          filters:
+            tags:
+              only: /.*/
+      - test:
+          requires:
+            - get_data
+            - build
+          filters:
+            tags:
+              only: /.*/
+      - deploy:
+          requires:
+            - test
+          filters:
+            branches:
+              only: master
+            tags:
+              only: /.*/

Dockerfile

@@ -77,10 +77,10 @@ ENV LANG=C.UTF-8
 ENV LC_ALL=C.UTF-8
 
 
-RUN pip install nibabel
-RUN pip install pybids
-RUN pip install duecredit
-
+RUN pip install nibabel==2.2.0
+RUN pip install pybids==0.3 grabbit==0.0.8
+RUN pip install duecredit==0.6.3
+RUN pip install scikit-learn==0.17.1
 
 COPY . /code/
 RUN cd /code && ls && pip install -e .