[ENH] Move to CircleCI (#28)

.circleci/config.yml

@@ -0,0 +1,390 @@
+version: 2
+jobs:
+
+ build:
+ environment:
+ TZ: "/usr/share/zoneinfo/America/New_York"
+ SCRATCH: "/scratch"
+ docker:
+ - image: docker:18.06.1-ce-git
+ working_directory: /tmp/src/BOnD
+ steps:
+ - checkout
+ - run:
+ name: Install parallel gzip and python3
+ command: |
+ apk add --no-cache pigz python3 tar
+ - restore_cache:
+ keys:
+ - docker-v1-{{ .Branch }}-{{ .Revision }}
+ - docker-v1-{{ .Branch }}-
+ - docker-v1-master-
+ - docker-v1-
+ 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
+ docker images
+ fi
+ - run:
+ name: Build Docker image
+ no_output_timeout: 3h
+ command: |
+ # Build docker image
+ e=1 && for i in {1..5}; do
+ docker build \
+ --cache-from=pennlinc/bond \
+ --rm=false \
+ -t pennlinc/bond:latest \
+ --build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` \
+ --build-arg VCS_REF=`git rev-parse --short HEAD` . \
+ && e=0 && break || sleep 15
+ done && [ "$e" -eq "0" ]
+
+ - run:
+ name: Docker save
+ no_output_timeout: 40m
+ command: |
+ mkdir -p /tmp/cache
+ docker save pennlinc/bond:latest \
+ | pigz -3 > /tmp/cache/docker.tar.gz
+
+ - save_cache:
+ key: docker-v1-{{ .Branch }}-{{ .Revision }}-{{ epoch }}
+ paths:
+ - /tmp/cache/docker.tar.gz
+
+
+ setup_conda:
+ machine:
+ image: ubuntu-1604:202004-01
+ steps:
+ - run:
+ name: install miniconda
+ command: |
+ cd /tmp
+ export MINICONDA=/tmp/miniconda
+ export PATH="$MINICONDA/bin:$PATH"
+ wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
+ bash miniconda.sh -b -f -p $MINICONDA
+ conda config --set always_yes yes
+ conda update conda
+ conda info -a
+ conda create -n bond python=3.7
+ source activate bond
+ conda install -c conda-forge -y datalad
+
+ - persist_to_workspace:
+ root: /tmp
+ paths:
+ - miniconda
+
+
+ install_and_test:
+ machine:
+ image: ubuntu-1604:202004-01
+ working_directory: /home/circleci/src/BOnD
+ steps:
+ - checkout:
+ path: /home/circleci/src/BOnD
+
+ - attach_workspace:
+ at: /tmp
+
+ - restore_cache:
+ keys:
+ - docker-v1-{{ .Branch }}-{{ .Revision }}
+
+ - run:
+ name: Load Docker image layer cache
+ no_output_timeout: 30m
+ command: |
+ docker info
+ set +o pipefail
+ if [ -f /tmp/cache/docker.tar.gz ]; then
+ sudo apt update && sudo apt -y install pigz
+ pigz -d --stdout /tmp/cache/docker.tar.gz | docker load
+ docker images
+ fi
+
+ - run:
+ name: Install BOnD
+ command: |
+ export PATH=/tmp/miniconda/bin:$PATH
+ source activate bond
+ pip install .[all]
+
+ - run:
+ name: Run PyTest
+ command: |
+ export PATH=/tmp/miniconda/bin:$PATH
+ source activate bond
+ py.test -sv tests
+
+ build_docs:
+ docker:
+ - image: circleci/python:3.7.4
+ working_directory: /tmp/src/BOnD
+ steps:
+ - checkout
+ - run:
+ name: Check whether build should be skipped
+ command: |
+ if [[ "$( git log --format=oneline -n 1 $CIRCLE_SHA1 | grep -i -E '\[skip[ _]?docs\]' )" != "" ]]; then
+ echo "Skipping doc building job"
+ circleci step halt
+ fi
+
+ - run:
+ name: Check Python version and upgrade pip
+ command: |
+ python --version
+ sudo python -m pip install -U pip 
+ sudo pip install flake8
+
+ - run:
+ name: Lint code with flake8
+ command: |
+ flake8 bond
+
+ - run:
+ name: Install BOnD.
+ command: sudo python -m pip install ".[doc]" --no-cache-dir --progress-bar off
+
+ - run:
+ name: Build documentation
+ no_output_timeout: 45m
+ command: |
+ make SPHINXOPTS="-W" -C docs html
+ - store_artifacts:
+ path: /tmp/src/BOnD/docs/_build/html
+
+ deploy_docker:
+ machine:
+ image: circleci/classic:201711-01
+ working_directory: /tmp/src/BOnD
+ steps:
+ - checkout:
+ path: /home/circleci/src/BOnD
+ - run:
+ name: Check whether build should be skipped
+ command: |
+ cd /home/circleci/src/BOnD
+ if [[ "$( git log --format='format:%s' -n 1 $CIRCLE_SHA1 | grep -i -E '^docs?(\(\w+\))?:' )" != "" ]]; then
+ echo "Only docs build"
+ circleci step halt
+ fi
+ - restore_cache:
+ keys:
+ - docker-v1-{{ .Branch }}-{{ .Revision }}
+ - 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
+ sudo apt update && sudo apt -y install pigz
+ pigz -d --stdout /tmp/cache/docker.tar.gz | docker load
+ docker images
+ fi
+ - run:
+ name: Deploy to Docker Hub
+ no_output_timeout: 40m
+ command: |
+ if [[ -n "$DOCKER_PASS" ]]; then
+ docker login -u $DOCKER_USER -p $DOCKER_PASS
+ docker tag pennlinc/BOnD pennlinc/BOnD:unstable
+ docker push pennlinc/BOnD:unstable
+ if [[ -n "$CIRCLE_TAG" ]]; then
+ docker push pennlinc/BOnD:latest
+ docker tag pennlinc/BOnD pennlinc/BOnD:$CIRCLE_TAG
+ docker push pennlinc/BOnD:$CIRCLE_TAG
+ fi
+ fi
+
+ test_deploy_pypi:
+ docker:
+ - image: circleci/python:3.7.4
+ working_directory: /tmp/src/BOnD
+ steps:
+ - checkout
+ - run:
+ name: Build BOnD
+ command: |
+ pip install --user twine # For use in checking distributions
+ THISVERSION=$( python3 get_version.py )
+ THISVERSION=${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}" > BOnD/VERSION
+ python setup.py sdist
+ pip wheel --no-deps -w dist/ .
+ - store_artifacts:
+ path: /tmp/src/BOnD/dist
+ - run:
+ name: Check sdist distribution
+ command: |
+ THISVERSION=$( python get_version.py )
+ THISVERSION=${THISVERSION%.dirty*}
+ THISVERSION=${CIRCLE_TAG:-$THISVERSION}
+ twine check dist/BOnD*.tar.gz
+ virtualenv --python=python sdist
+ source sdist/bin/activate
+ pip install --progress-bar off --upgrade "pip>=19.1" numpy
+ pip install dist/BOnD*.tar.gz
+ which BOnD | grep sdist\\/bin
+ INSTALLED_VERSION=$(BOnD --version)
+ INSTALLED_VERSION=${INSTALLED_VERSION%$'\r'}
+ INSTALLED_VERSION=${INSTALLED_VERSION#*"BOnD 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/BOnD*.whl
+ virtualenv --python=python wheel
+ source wheel/bin/activate
+ pip install dist/BOnD*.whl
+ which BOnD | grep wheel\\/bin
+ INSTALLED_VERSION=$(BOnD --version)
+ INSTALLED_VERSION=${INSTALLED_VERSION%$'\r'}
+ INSTALLED_VERSION=${INSTALLED_VERSION#*"BOnD v"}
+ echo "VERSION: \"$THISVERSION\""
+ echo "INSTALLED: \"$INSTALLED_VERSION\""
+ test "$INSTALLED_VERSION" = "$THISVERSION"
+ - run:
+ name: Build BOnD-container
+ 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}'/" qsiprep_docker.py
+ python setup.py sdist
+ pip wheel --no-deps -w dist/ .
+ - store_artifacts:
+ path: /tmp/src/BOnD/wrapper/dist
+
+ deploy_pypi:
+ docker:
+ - image: circleci/python:3.7.4
+ working_directory: /tmp/src/BOnD
+ steps:
+ - checkout
+ - run:
+ name: Build BOnD
+ command: |
+ THISVERSION=$( python get_version.py )
+ virtualenv --python=python build
+ source build/bin/activate
+ pip install --upgrade "pip>=19.1" numpy
+ echo "${CIRCLE_TAG:-$THISVERSION}" > BOnD/VERSION
+ python setup.py sdist
+ pip wheel --no-deps -w dist/ .
+ - run:
+ name: Build BOnD-container
+ command: |
+ THISVERSION=$( 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}'/" qsiprep_docker.py
+ python setup.py sdist
+ pip wheel --no-deps -w dist/ .
+ - run:
+ name: Upload packages to PyPI
+ command: |
+ pip install --user twine
+ pip install --user --upgrade importlib-metadata
+ twine upload dist/BOnD*gz wrapper/dist/BOnD*
+
+ deployable:
+ docker:
+ - image: busybox:latest
+ steps:
+ - run: echo Deploying!
+
+
+workflows:
+ version: 2
+ build_test_deploy:
+ jobs:
+ - build:
+ filters:
+ tags:
+ only: /.*/
+
+ - setup_conda:
+ filters:
+ branches:
+ ignore:
+ - /tests?\/.*/
+ - /docker\/.*/
+ tags:
+ only: /.*/
+
+ - install_and_test:
+ requires:
+ - build
+ - setup_conda
+ filters:
+ branches:
+ ignore:
+ - /tests?\/.*/
+ - /docker\/.*/
+ tags:
+ only: /.*/
+
+ - build_docs:
+ filters:
+ branches:
+ ignore:
+ - /tests?\/.*/
+ - /docker\/.*/
+ tags:
+ only: /.*/
+
+ - deployable:
+ requires:
+ - build_docs
+ - install_and_test
+ filters:
+ branches:
+ only: master
+ tags:
+ only: /.*/
+
+ - deploy_docker:
+ requires:
+ - deployable
+ filters:
+ branches:
+ only: master
+ tags:
+ only: /.*/
+
+ - deploy_pypi:
+ requires:
+ - deployable
+ filters:
+ branches:
+ ignore: /.*/
+ tags:
+ only: /.*/