update dockerfile apt repository sources for xenial #119
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| # watch to see if github expands the github context to provide a property similar to github.repository | |
| # but docker friendly | |
| # https://github.community/t5/GitHub-Actions/Feature-Request-context-property-similar-to-github-repository/m-p/38886#M3561 | |
| name: Continuous Integration | |
| on: [push] | |
| env: | |
| # github registry currently requires authentication, so we use it for caching the testing image, but not for release | |
| # images. | |
| REGISTRY: docker.pkg.github.com | |
| TEST_IMAGE_BRANCH: ${{ github.repository }}/testing:${{ github.ref }} | |
| # the following three variables are unused | |
| TEST_IMAGE_LATEST: ${{ github.repository }}/testing:latest | |
| BIDSAPP_IMAGE_LATEST: ${{ github.repository }}/bidsapp:latest | |
| BIDSAPP_IMAGE_TAG: ${{ github.repository }}/bidsapp:${{ github.ref }} | |
| # use dockerhub for release images | |
| TEST_IMAGE_LATEST_DOCKERHUB: akuurstr/qsm_sstv:testing | |
| BIDSAPP_IMAGE_LATEST_DOCKERHUB: akuurstr/qsm_sstv:latest | |
| BIDSAPP_IMAGE_TAG_DOCKERHUB: akuurstr/qsm_sstv:${{ github.ref }} | |
| jobs: | |
| build: | |
| name: update testing docker image if necessary | |
| # jobs run in virtual environments, actions run in containers | |
| # action containers are cached behind the scenes | |
| # but since the ubuntu VM is able to execute actions in docker, | |
| # it must have docker installed. So we can probably run our docker | |
| # build in the VM shell and avoid the overhead of creating | |
| # tailored actions in an action container. | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@master | |
| - name: Dump GitHub context | |
| env: | |
| GITHUB_CONTEXT: ${{ toJson(github) }} | |
| run: echo "$GITHUB_CONTEXT" | |
| - name: load cache | |
| # note: docker image currently too large to save in cache? | |
| uses: actions/cache@v1 | |
| with: | |
| path: previous_docker_image | |
| key: previous-docker-image | |
| - name: reformat git-based container names for docker | |
| shell: bash | |
| run: | | |
| # include registry, convert to all lower case, remove /refs/heads/ from branch name | |
| # this is pretty simple and there are probably other repository and branch names that would break docker | |
| # also note the format to make env variables global to other steps: echo::set-env name={name}:{value} | |
| reformat(){ | |
| echo "$1" | tr '[:upper:]' '[:lower:]' | sed -e "s/refs\/heads\///g" | sed -e "s/refs\/tags\///g" | |
| } | |
| echo "TEST_IMAGE_BRANCH=$(reformat ${REGISTRY}/${TEST_IMAGE_BRANCH})" >> "$GITHUB_ENV" | |
| echo "TEST_IMAGE_LATEST=$(reformat ${REGISTRY}/${TEST_IMAGE_LATEST})" >> "$GITHUB_ENV" | |
| echo "BIDSAPP_IMAGE_LATEST=$(reformat ${REGISTRY}/${BIDSAPP_IMAGE_LATEST})" >> "$GITHUB_ENV" | |
| echo "BIDSAPP_IMAGE_TAG=$(reformat ${REGISTRY}/${BIDSAPP_IMAGE_TAG})" >> "$GITHUB_ENV" | |
| echo "BIDSAPP_IMAGE_TAG_DOCKERHUB=$(reformat ${BIDSAPP_IMAGE_TAG_DOCKERHUB})" >> "$GITHUB_ENV" | |
| - name: login to github package registry | |
| run: | | |
| docker login $REGISTRY -u ${{ github.actor }} -p ${{ secrets.GITHUB_TOKEN }} | |
| - name: load previous testing image from either cache or package registry | |
| continue-on-error: true | |
| shell: bash | |
| run: | | |
| if docker load -i previous_docker_image/prev_image.tar; then | |
| echo "Loaded docker image from cache." | |
| else | |
| if docker pull ${TEST_IMAGE_BRANCH}; then | |
| echo "Pulled ${TEST_IMAGE_BRANCH}" | |
| else | |
| #docker pull ${TEST_IMAGE_LATEST} | |
| docker pull ${TEST_IMAGE_LATEST_DOCKERHUB} | |
| fi | |
| fi | |
| - name: build testing image | |
| run: | | |
| docker build \ | |
| --cache-from ${TEST_IMAGE_LATEST} \ | |
| --cache-from ${TEST_IMAGE_BRANCH} \ | |
| -t ${TEST_IMAGE_BRANCH} \ | |
| -f Dockerfile_testing . | |
| # export a docker image for caching | |
| docker save ${TEST_IMAGE_BRANCH} -o previous_docker_image/prev_image.tar | |
| - name: push testing image to github | |
| run: | | |
| docker push ${TEST_IMAGE_BRANCH} | |
| tests: | |
| name: test pipeline | |
| needs: [build] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@master | |
| - name: load cache | |
| # note: docker image currently too large to save in cache? | |
| uses: actions/cache@v1 | |
| with: | |
| path: previous_docker_image | |
| key: previous-docker-image | |
| - name: reformat git-based container names for docker | |
| shell: bash | |
| run: | | |
| # include registry, convert to all lower case, remove /refs/heads/ from branch name | |
| # this is pretty simple and there are probably other repository and branch names that would break docker | |
| # also note the format to make env variables global to other steps: echo::set-env name={name}:{value} | |
| reformat(){ | |
| echo "$1" | tr '[:upper:]' '[:lower:]' | sed -e "s/refs\/heads\///g" | sed -e "s/refs\/tags\///g" | |
| } | |
| echo ::set-env name=TEST_IMAGE_BRANCH::$(reformat ${REGISTRY}/${TEST_IMAGE_BRANCH}) | |
| echo ::set-env name=TEST_IMAGE_LATEST::$(reformat ${REGISTRY}/${TEST_IMAGE_LATEST}) | |
| echo ::set-env name=BIDSAPP_IMAGE_LATEST::$(reformat ${REGISTRY}/${BIDSAPP_IMAGE_LATEST}) | |
| echo ::set-env name=BIDSAPP_IMAGE_TAG::$(reformat ${REGISTRY}/${BIDSAPP_IMAGE_TAG}) | |
| echo ::set-env name=BIDSAPP_IMAGE_TAG_DOCKERHUB::$(reformat ${BIDSAPP_IMAGE_TAG_DOCKERHUB}) | |
| - name: login to github package registry | |
| run: | | |
| docker login $REGISTRY -u ${{ github.actor }} -p ${{ secrets.GITHUB_TOKEN }} | |
| - name: load previous testing image from either cache or package registry | |
| shell: bash | |
| run: | | |
| if docker load -i previous_docker_image/prev_image.tar; then | |
| echo "Loaded docker image from cache." | |
| else | |
| docker pull ${TEST_IMAGE_BRANCH} | |
| fi | |
| - name: run tests | |
| shell: bash | |
| run: | | |
| docker run -v `pwd`:/code ${TEST_IMAGE_BRANCH} /bin/bash -c \ | |
| "virtualenv venv;\ | |
| source venv/bin/activate;\ | |
| pip install -r /code/requirements.txt;\ | |
| export PYTHON_PATH=/code;\ | |
| python -m unittest discover /code/test" | |
| release_tagged: | |
| name: push version-tagged docker images | |
| if: startsWith(github.ref, 'refs/tags/') | |
| needs: [build, tests] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: load cache | |
| # note: docker image currently too large to save in cache? | |
| uses: actions/cache@v1 | |
| with: | |
| path: previous_docker_image | |
| key: previous-docker-image | |
| - name: reformat git-based container names for docker | |
| shell: bash | |
| run: | | |
| reformat(){ | |
| echo "$1" | tr '[:upper:]' '[:lower:]' | sed -e "s/refs\/heads\///g" | sed -e "s/refs\/tags\///g" | |
| } | |
| echo ::set-env name=TEST_IMAGE_BRANCH::$(reformat ${REGISTRY}/${TEST_IMAGE_BRANCH}) | |
| echo ::set-env name=TEST_IMAGE_LATEST::$(reformat ${REGISTRY}/${TEST_IMAGE_LATEST}) | |
| echo ::set-env name=BIDSAPP_IMAGE_LATEST::$(reformat ${REGISTRY}/${BIDSAPP_IMAGE_LATEST}) | |
| echo ::set-env name=BIDSAPP_IMAGE_TAG::$(reformat ${REGISTRY}/${BIDSAPP_IMAGE_TAG}) | |
| echo ::set-env name=BIDSAPP_IMAGE_TAG_DOCKERHUB::$(reformat ${BIDSAPP_IMAGE_TAG_DOCKERHUB}) | |
| - name: login to github package registry | |
| run: | | |
| docker login $REGISTRY -u ${{ github.actor }} -p ${{ secrets.GITHUB_TOKEN }} | |
| - name: load previous testing image from either cache or package registry | |
| shell: bash | |
| run: | | |
| if docker load -i previous_docker_image/prev_image.tar; then | |
| echo "Loaded docker image from cache." | |
| else | |
| docker pull ${TEST_IMAGE_BRANCH} | |
| fi | |
| # checkout file: Dockerfile_bids_app | |
| - uses: actions/checkout@master | |
| - name: release tagged bids app image to dockerhub (because github registry requires authentication) | |
| run: | | |
| docker login -u ${{ secrets.DOCKERHUB_USER }} -p ${{ secrets.DOCKERHUB_TOKEN }} | |
| docker tag ${TEST_IMAGE_BRANCH} ${TEST_IMAGE_LATEST_DOCKERHUB} | |
| docker push ${TEST_IMAGE_LATEST_DOCKERHUB} | |
| docker build \ | |
| --cache-from ${TEST_IMAGE_BRANCH} \ | |
| -t ${BIDSAPP_IMAGE_TAG_DOCKERHUB} \ | |
| -f Dockerfile_bids_app . | |
| docker push ${BIDSAPP_IMAGE_TAG_DOCKERHUB} | |
| release_latest: | |
| name: push latest docker images | |
| if: github.ref == 'refs/heads/master' | |
| needs: [build, tests] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: load cache | |
| # note: docker image currently too large to save in cache? | |
| uses: actions/cache@v1 | |
| with: | |
| path: previous_docker_image | |
| key: previous-docker-image | |
| - name: reformat git-based container names for docker | |
| shell: bash | |
| run: | | |
| reformat(){ | |
| echo "$1" | tr '[:upper:]' '[:lower:]' | sed -e "s/refs\/heads\///g" | sed -e "s/refs\/tags\///g" | |
| } | |
| echo ::set-env name=TEST_IMAGE_BRANCH::$(reformat ${REGISTRY}/${TEST_IMAGE_BRANCH}) | |
| echo ::set-env name=TEST_IMAGE_LATEST::$(reformat ${REGISTRY}/${TEST_IMAGE_LATEST}) | |
| echo ::set-env name=BIDSAPP_IMAGE_LATEST::$(reformat ${REGISTRY}/${BIDSAPP_IMAGE_LATEST}) | |
| echo ::set-env name=BIDSAPP_IMAGE_TAG::$(reformat ${REGISTRY}/${BIDSAPP_IMAGE_TAG}) | |
| echo ::set-env name=BIDSAPP_IMAGE_TAG_DOCKERHUB::$(reformat ${BIDSAPP_IMAGE_TAG_DOCKERHUB}) | |
| - name: login to github package registry | |
| run: | | |
| docker login $REGISTRY -u ${{ github.actor }} -p ${{ secrets.GITHUB_TOKEN }} | |
| - name: load previous testing image from either cache or package registry | |
| shell: bash | |
| run: | | |
| if docker load -i previous_docker_image/prev_image.tar; then | |
| echo "Loaded docker image from cache." | |
| else | |
| docker pull ${TEST_IMAGE_BRANCH} | |
| fi | |
| - name: release testing image to github | |
| shell: bash | |
| if: 0 | |
| run: | | |
| docker tag ${TEST_IMAGE_BRANCH} ${TEST_IMAGE_LATEST} | |
| docker push ${TEST_IMAGE_LATEST} | |
| - name: release testing image to dockerhub (because github registry requires authentication) | |
| run: | | |
| docker login -u ${{ secrets.DOCKERHUB_USER }} -p ${{ secrets.DOCKERHUB_TOKEN }} | |
| docker tag ${TEST_IMAGE_BRANCH} ${TEST_IMAGE_LATEST_DOCKERHUB} | |
| docker push ${TEST_IMAGE_LATEST_DOCKERHUB} | |
| # checkout file: Dockerfile_bids_app | |
| - uses: actions/checkout@master | |
| - name: release bidsapp image to dockerhub (because github registry requires authentication) | |
| run: | | |
| docker login -u ${{ secrets.DOCKERHUB_USER }} -p ${{ secrets.DOCKERHUB_TOKEN }} | |
| docker build \ | |
| --cache-from ${TEST_IMAGE_LATEST} \ | |
| --cache-from ${TEST_IMAGE_LATEST_DOCKERHUB} \ | |
| -t ${BIDSAPP_IMAGE_LATEST_DOCKERHUB} \ | |
| -f Dockerfile_bids_app . | |
| docker push ${BIDSAPP_IMAGE_LATEST_DOCKERHUB} | |