Merge pull request #1569 from FCP-INDI/develop

Release v1.8.1

Author: sgiavasis

.circleci/config.yml

@@ -1,247 +1,15 @@
+setup: true
 version: 2.1
-
-commands:
-  build-images:
-    parameters:
-      variant:
-        type: string
-        default: ""
-    steps:
-      - set-up-variant:
-          variant: "<< parameters.variant >>"
-      - run:
-          name: "Building Docker image"
-          command: |
-            docker build -t fcpindi/c-pac:${DOCKER_TAG} . ${DOCKERFILE}
-            docker save fcpindi/c-pac:${DOCKER_TAG} | gzip > ${DOCKER_TARBALL}.tar.gz
-          no_output_timeout: 5h
-      - run:
-          name: "Starting local registry"
-          command: docker run -d -p 5000:5000 --restart=always --name registry registry:2
-      - install-singularity-requirements
-      - when:
-          condition:
-            or:
-            - equal: [ "", "<< parameters.variant >>" ]
-            - equal: [ "lite", "<< parameters.variant >>" ]
-          steps:
-            - run: 
-                name: "Cloning Singularity 2.5.2"
-                command: git clone -b 2.5.2 https://github.com/sylabs/singularity
-      - set-up-singularity
-      - run:
-          name: "Building Singularity image from Docker image"
-          command: |
-            docker load < ${DOCKER_TARBALL}.tar.gz
-            docker tag fcpindi/c-pac:${CIRCLE_BRANCH//\//_}${VARIANT} localhost:5000/fcpindi/c-pac:${CIRCLE_BRANCH//\//_}${VARIANT}
-            docker push localhost:5000/fcpindi/c-pac:${CIRCLE_BRANCH//\//_}${VARIANT}
-            SINGULARITY_NOHTTPS=1 singularity build cpac-singularity-image${VARIANT}.simg docker://localhost:5000/fcpindi/c-pac:${CIRCLE_BRANCH//\//_}${VARIANT}
-          no_output_timeout: 5h
-  check-for-built-images:
-    steps:
-      - run:
-          name: "Checking for locally built images"
-          command: |
-            if [[ ! -f cpac-docker-image.tar.gz || ! -f cpac-singularity-image.simg ]]
-            then
-              circleci step halt
-            fi
-  configure-git-user:
-    steps:
-      - add_ssh_keys:
-          fingerprints:
-            - "12:bc:f2:e4:31:cc:72:54:54:bc:f5:5b:89:e6:d8:ee"
-      - run:
-          name: "Configuring git user"
-          command: |
-            sudo apt-key adv --recv-keys --keyserver keyserver.ubuntu.com 78BD65473CB3BD13
-            curl -L https://packagecloud.io/circleci/trusty/gpgkey | sudo apt-key add -
-            sudo apt-get update
-            sudo apt-get install git -y
-            git config --global user.email "${CIRCLE_USERNAME}@users.noreply.github.com"
-            git config --global user.name "${CIRCLE_USERNAME} @ CircleCI"
-  get-sample-bids-data:
-    steps:
-      - run:
-          name: Getting Sample BIDS Data
-          command: git clone https://github.com/bids-standard/bids-examples.git
-  set-python-version:
-    steps:
-      - run:
-          name: "Setting Python Version"
-          command: |
-            cd /opt/circleci/.pyenv/plugins/python-build/../.. && git pull && cd -
-            pyenv install -v 3.7.9
-            pyenv global 3.7.9
-  install-singularity-requirements:
-    steps:
-      - run:
-          name: "Installing Singularity requirements"
-          command: |
-           sudo apt-get update && sudo apt-get install flawfinder squashfs-tools uuid-dev libuuid1 libffi-dev libssl-dev libssl1.1 libarchive-dev libgpgme11-dev libseccomp-dev -y
-  run-pytest-docker:
-    steps:
-      - run:
-          name: Running pytest on Docker image
-          command: |
-            docker load < cpac-docker-image.tar.gz
-            docker run -dit -P -v /home/circleci/project/test-results:/code/test-results -v /home/circleci/project/htmlcov:/code/htmlcov --entrypoint=/bin/bash --name docker_test fcpindi/c-pac:${DOCKER_TAG}
-            docker exec docker_test /bin/bash ./code/dev/circleci_data/test_in_image.sh
-  set-up-singularity:
-    steps:
-      - run:
-         name: "Setting up Singularity"
-         command: |
-           cd singularity
-           ./autogen.sh
-           ./configure --prefix=/usr/local --sysconfdir=/etc
-           make
-           sudo make install
-           cd ..
-  set-up-variant:
-    parameters:
-      variant:
-        type: string
-    steps:
-      - run:
-          name: "Setting up variant"
-          command: |
-            DOCKER_TARBALL="cpac-docker-image"
-            if [[ -n "<< parameters.variant >>" ]]
-            then
-              DOCKERFILE="variant-<< parameters.variant >>.Dockerfile"
-              if [[ -f ${DOCKERFILE} ]]
-              then
-                sed -i "s|:latest|:${CIRCLE_BRANCH//\//_}|g" ${DOCKERFILE}
-              fi
-              DOCKER_TARBALL="${DOCKER_TARBALL}-<< parameters.variant >>"
-              VARIANT="-<< parameters.variant >>"
-              echo "export DOCKERFILE=\"-f ${DOCKERFILE}\"" >> $BASH_ENV
-            fi
-            echo "export DOCKER_TARBALL=${DOCKER_TARBALL}" >> $BASH_ENV
-            echo "export VARIANT=${VARIANT}" >> $BASH_ENV
-            DOCKER_TAG=${CIRCLE_BRANCH//\//_}${VARIANT}
-            echo "export DOCKER_TAG=${DOCKER_TAG}" >> $BASH_ENV
-  test-singularity-installation:
-    steps:
-      - run:
-          name: Testing Singularity installation
-          command: |
-            pip install -r dev/circleci_data/requirements.txt
-            coverage run -m pytest --junitxml=test-results/junit.xml --continue-on-collection-errors  dev/circleci_data/test_install.py
-
-jobs:
-  pytest-docker:
-    parameters:
-      variant:
-        type: string
-        default: ""
-    machine:
-      image: ubuntu-2004:202010-01
-    steps:
-      - attach_workspace:
-          at: /home/circleci/
-      - set-up-variant:
-          variant: "<< parameters.variant >>"
-      - check-for-built-images
-      - set-python-version
-      - get-sample-bids-data
-      - run-pytest-docker
-      - store_test_results:
-          path: test-results
-      - store_artifacts:
-          path: test-results
-      - store_artifacts:
-          path: htmlcov
-
-  pytest-singularity:
-    machine:
-      image: ubuntu-2004:202010-01
-    steps:
-      - attach_workspace:
-          # Must be absolute path or relative path from working_directory
-          at: /home/circleci/
-      - check-for-built-images
-      - set-python-version
-      - install-singularity-requirements
-      - set-up-singularity
-      - test-singularity-installation
-
-  build:
-    machine:
-      image: ubuntu-2004:202010-01
-    steps:
-      - checkout
-      - set-python-version
-      - configure-git-user
-      - run:
-          name: "Checking if version needs updated"
-          # update version if version needs updated, otherwise just move on
-          command: |
-            COMMIT_MESSAGE=$(git log -1 --pretty=%B)
-            if [[ ! "$COMMIT_MESSAGE" == *"Update version to"* ]]
-            then
-              cd $HOME/project/CPAC
-              VERSION=$(python -c "from info import __version__; print('.'.join(('.'.join(__version__[::-1].split('-')[1].split('.')[1:])[::-1], __version__.split('-')[1])) if '-' in __version__ else __version__)")
-              cd ..
-              echo "v${VERSION}" > version
-              sed -i -r "s/^(# [Vv]ersion ).*$/# Version ${VERSION}/g" dev/docker_data/default_pipeline.yml
-              find ./CPAC/resources/configs -name "*.yml" -exec sed -i -r "s/^(# [Vv]ersion ).*$/# Version ${VERSION}/g" {} \;
-              git add version CPAC/resources/configs dev/docker_data/default_pipeline.yml
-              if [[ ! -z $(git diff origin/${CIRCLE_BRANCH}) ]]
-              then
-                git commit -m ":bookmark: Update version to ${VERSION} ($COMMIT_MESSAGE)"
-                git push origin HEAD:${CIRCLE_BRANCH} || true
-                circleci step halt
-              fi
-              cd ..
-            fi
-      - build-images
-      - store_artifacts:
-          path: cpac-docker-image.tar.gz
-      - store_artifacts:
-          path: cpac-singularity-image.simg
-      - persist_to_workspace:
-          root: /home/circleci/
-          paths:
-            - cpac-docker-image.tar.gz
-            - cpac-singularity-image.simg
-            - project
-  build-lite:
-    machine:
-      image: ubuntu-2004:202010-01
-    steps:
-      - checkout
-      - set-python-version
-      - build-images:
-          variant: lite
-      - store_artifacts:
-          path: cpac-docker-image-lite.tar.gz
-      - store_artifacts:
-          path: cpac-singularity-image-lite.simg
-
+orbs:
+  continuation: circleci/[email protected]
 workflows:
-  version: 2
-  build-and-test:
+  setup:
     jobs:
-      - build:
-          name: "Build images"
-      - build-lite:
-          name: "Build lite variant images"
-      - pytest-docker:
-          name: "Test in Docker"
-          requires:
-            - "Build images"
-      - pytest-docker:
-          name: "Test lite variant in Docker"
-          requires:
-            - "Build lite variant images"
-          variant: lite
-      - pytest-singularity:
-          name: "Test in Singularity"
-          requires:
-            - "Build images"
-      - pytest-singularity:
-          name: "Test lite variant in Singularity"
-          requires:
-            - "Build lite variant images"
+      - continuation/continue:
+          configuration_path: ".circleci/main.yml"
+          parameters: /home/circleci/test.json
+          pre-steps:
+            - run:
+                command: |
+                  echo '{ "owner": "'${CIRCLE_PROJECT_USERNAME}'", "branch": "'${CIRCLE_BRANCH}'" }' >> /home/circleci/test.json
+