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Initial commit for open-sourcing
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‎.dockerignore

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**/.local/
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**/node_modules/
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**/dist/
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**/data/
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**/log/
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**/input/
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**/output/

‎.github/workflows/ci-basel.yaml

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name: Basel Connector-Build, Test & Publish Docker
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on:
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push:
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paths:
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- 'packages/neherlab-covid-19-scenarios/**'
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- 'packages/api/**'
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env:
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IMAGE_NAME: neherlab-covid-19-scenarios-connector
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jobs:
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# Run tests.
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# See also https://docs.docker.com/docker-hub/builds/automated-testing/
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test:
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runs-on: ubuntu-latest
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defaults:
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run:
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working-directory: packages/neherlab-covid-19-scenarios
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steps:
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- uses: actions/checkout@v2
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- name: Log into registry for Imperial images
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run: echo "${{ secrets.GITHUB_PAT }}" | docker login docker.pkg.github.com -u ${{ secrets.GITHUB_PAT_USER }} --password-stdin
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- name: Run tests
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run: docker-compose build test
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publish:
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needs: test
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runs-on: ubuntu-latest
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defaults:
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run:
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working-directory: packages/neherlab-covid-19-scenarios
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strategy:
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fail-fast: true
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steps:
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- name: Checkout
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uses: actions/checkout@v1
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- name: Log into registry for Docker images
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run: echo "${{ secrets.GITHUB_PAT }}" | docker login docker.pkg.github.com -u ${{ secrets.GITHUB_PAT_USER }} --password-stdin
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- name: Build image
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run: docker-compose build release
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- name: Log into registry
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run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login docker.pkg.github.com -u ${{ github.actor }} --password-stdin
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- name: Push image (Local)
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run: |
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IMAGE_ID=docker.pkg.github.com/${{ github.repository }}/$IMAGE_NAME
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# Change all uppercase to lowercase
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IMAGE_ID=$(echo $IMAGE_ID | tr '[A-Z]' '[a-z]')
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# Strip git ref prefix (refs/heads/ or refs/tags/) from version
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# but keep the rest of the ref. Replaces / with - to make the package name valid.
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# Do not attempt to obtain the version number from vx.y.z tags:
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# this is handled by the publish_version workflow.
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VERSION=$(echo "${{ github.ref }}" | sed -e 's,refs/\(heads\|tags\)/\(.*\),\2,' | tr '/' '-')
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# Always tag with git sha or version tag
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echo IMAGE_ID=$IMAGE_ID
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echo VERSION=$VERSION
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docker tag image $IMAGE_ID:$VERSION
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docker push $IMAGE_ID:$VERSION
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# Use Docker `latest` tag convention for master.
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[ "$VERSION" == "master" ] && VERSION=latest
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echo IMAGE_ID=$IMAGE_ID
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echo VERSION=$VERSION
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docker tag image $IMAGE_ID:$VERSION
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docker push $IMAGE_ID:$VERSION

‎.github/workflows/ci-mc19.yaml

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name: MC19 Connector-Build, Test & Publish Docker
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on:
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push:
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paths:
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- 'packages/modelingcovid-covidmodel/**'
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env:
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IMAGE_NAME: modelingcovid-covidmodel-connector
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jobs:
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# Run tests.
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# See also https://docs.docker.com/docker-hub/builds/automated-testing/
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test:
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runs-on: ubuntu-latest
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defaults:
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run:
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working-directory: packages/modelingcovid-covidmodel
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steps:
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- uses: actions/checkout@v2
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- name: Log into registry for Docker images
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run: echo "${{ secrets.GITHUB_PAT }}" | docker login docker.pkg.github.com -u ${{ secrets.GITHUB_PAT_USER }} --password-stdin
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- name: Run tests
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run: docker-compose build test
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publish:
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needs: test
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runs-on: ubuntu-latest
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defaults:
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run:
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working-directory: packages/modelingcovid-covidmodel
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strategy:
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fail-fast: true
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steps:
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- name: Checkout
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uses: actions/checkout@v1
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- name: Log into registry for Docker images
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run: echo "${{ secrets.GITHUB_PAT }}" | docker login docker.pkg.github.com -u ${{ secrets.GITHUB_PAT_USER }} --password-stdin
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- name: Build image
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run: docker-compose build release
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- name: Log into registry
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run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login docker.pkg.github.com -u ${{ github.actor }} --password-stdin
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- name: Push image (Local)
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run: |
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IMAGE_ID=docker.pkg.github.com/${{ github.repository }}/$IMAGE_NAME
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# Change all uppercase to lowercase
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IMAGE_ID=$(echo $IMAGE_ID | tr '[A-Z]' '[a-z]')
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# Strip git ref prefix (refs/heads/ or refs/tags/) from version
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# but keep the rest of the ref. Replaces / with - to make the package name valid.
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# Do not attempt to obtain the version number from vx.y.z tags:
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# this is handled by the publish_version workflow.
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VERSION=$(echo "${{ github.ref }}" | sed -e 's,refs/\(heads\|tags\)/\(.*\),\2,' | tr '/' '-')
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# Always tag with git sha or version tag
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echo IMAGE_ID=$IMAGE_ID
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echo VERSION=$VERSION
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docker tag image $IMAGE_ID:$VERSION
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docker push $IMAGE_ID:$VERSION
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# Use Docker `latest` tag convention for master.
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[ "$VERSION" == "master" ] && VERSION=latest
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echo IMAGE_ID=$IMAGE_ID
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echo VERSION=$VERSION
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docker tag image $IMAGE_ID:$VERSION
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docker push $IMAGE_ID:$VERSION

‎.github/workflows/ci-mrc-ide-covidsim.yaml

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name: MRC-IDE CovidSim Connector-Build, Test & Publish Docker
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on:
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push:
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paths:
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- 'packages/mrc-ide-covidsim/**'
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- 'packages/api/**'
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env:
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IMAGE_NAME: mrc-ide-covidsim-connector
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jobs:
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# Run tests.
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# See also https://docs.docker.com/docker-hub/builds/automated-testing/
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test:
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runs-on: ubuntu-latest
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defaults:
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run:
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working-directory: packages/mrc-ide-covidsim
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steps:
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- uses: actions/checkout@v2
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- name: Log into registry for Docker images
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run: echo "${{ secrets.GITHUB_PAT }}" | docker login docker.pkg.github.com -u ${{ secrets.GITHUB_PAT_USER }} --password-stdin
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- name: Run tests
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run: docker-compose build test
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publish:
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needs: test
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runs-on: ubuntu-latest
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defaults:
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run:
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working-directory: packages/mrc-ide-covidsim
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strategy:
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fail-fast: true
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steps:
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- name: Checkout
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uses: actions/checkout@v1
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- name: Log into registry for Imperial images
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run: echo "${{ secrets.GITHUB_PAT }}" | docker login docker.pkg.github.com -u ${{ secrets.GITHUB_PAT_USER }} --password-stdin
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- name: Build image
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run: docker-compose build release
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- name: Log into registry
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run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login docker.pkg.github.com -u ${{ github.actor }} --password-stdin
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- name: Push image (Local)
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run: |
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IMAGE_ID=docker.pkg.github.com/${{ github.repository }}/$IMAGE_NAME
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# Change all uppercase to lowercase
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IMAGE_ID=$(echo $IMAGE_ID | tr '[A-Z]' '[a-z]')
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# Strip git ref prefix (refs/heads/ or refs/tags/) from version
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# but keep the rest of the ref. Replaces / with - to make the package name valid.
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# Do not attempt to obtain the version number from vx.y.z tags:
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# this is handled by the publish_version workflow.
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VERSION=$(echo "${{ github.ref }}" | sed -e 's,refs/\(heads\|tags\)/\(.*\),\2,' | tr '/' '-')
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# Always tag with git sha or version tag
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echo IMAGE_ID=$IMAGE_ID
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echo VERSION=$VERSION
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docker tag image $IMAGE_ID:$VERSION
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docker push $IMAGE_ID:$VERSION
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# Use Docker `latest` tag convention for master.
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[ "$VERSION" == "master" ] && VERSION=latest
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echo IMAGE_ID=$IMAGE_ID
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echo VERSION=$VERSION
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docker tag image $IMAGE_ID:$VERSION
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docker push $IMAGE_ID:$VERSION

‎.github/workflows/ci.yaml

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name: Model Runner-Build, Test & Publish Docker
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on:
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push:
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paths:
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- 'packages/model-runner/**'
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- 'packages/api/**'
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env:
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IMAGE_NAME: model-runner
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jobs:
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# Run tests.
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# See also https://docs.docker.com/docker-hub/builds/automated-testing/
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test:
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runs-on: ubuntu-latest
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defaults:
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run:
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working-directory: packages/model-runner
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steps:
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- uses: actions/checkout@v2
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- name: Log into registry for Docker images
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run: echo "${{ secrets.GITHUB_PAT }}" | docker login docker.pkg.github.com -u ${{ secrets.GITHUB_PAT_USER }} --password-stdin
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- name: Run tests
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run: docker-compose build test
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publish:
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needs: test
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runs-on: ubuntu-latest
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defaults:
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run:
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working-directory: packages/model-runner
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strategy:
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fail-fast: true
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steps:
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- name: Checkout
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uses: actions/checkout@v1
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- name: Log into registry for Docker images
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run: echo "${{ secrets.GITHUB_PAT }}" | docker login docker.pkg.github.com -u ${{ secrets.GITHUB_PAT_USER }} --password-stdin
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- name: Build image
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run: docker-compose build release
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- name: Log into registry
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run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login docker.pkg.github.com -u ${{ github.actor }} --password-stdin
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- name: Push image (Local)
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run: |
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IMAGE_ID=docker.pkg.github.com/${{ github.repository }}/$IMAGE_NAME
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# Change all uppercase to lowercase
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IMAGE_ID=$(echo $IMAGE_ID | tr '[A-Z]' '[a-z]')
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# Strip git ref prefix (refs/heads/ or refs/tags/) from version
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# but keep the rest of the ref. Replaces / with - to make the package name valid.
60+
# Do not attempt to obtain the version number from vx.y.z tags:
61+
# this is handled by the publish_version workflow.
62+
VERSION=$(echo "${{ github.ref }}" | sed -e 's,refs/\(heads\|tags\)/\(.*\),\2,' | tr '/' '-')
63+
# Always tag with git sha or version tag
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echo IMAGE_ID=$IMAGE_ID
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echo VERSION=$VERSION
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docker tag image $IMAGE_ID:$VERSION
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docker push $IMAGE_ID:$VERSION
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# Use Docker `latest` tag convention for master.
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[ "$VERSION" == "master" ] && VERSION=latest
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echo IMAGE_ID=$IMAGE_ID
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echo VERSION=$VERSION
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docker tag image $IMAGE_ID:$VERSION
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docker push $IMAGE_ID:$VERSION

‎.github/workflows/publish_version-basel.yaml

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name: Basel Connector-Publish Docker Images for Tags/Releases
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on:
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push:
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# Publish `neherlab-covid-19-scenarios/v1.2.3` tags as `neherlab-covid-19-scenarios-connector` releases.
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tags:
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- 'neherlab-covid-19-scenarios/v*'
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env:
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PACKAGE_NAME: neherlab-covid-19-scenarios
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IMAGE_NAME: neherlab-covid-19-scenarios-connector
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jobs:
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publish:
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runs-on: ubuntu-latest
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defaults:
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run:
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working-directory: packages/neherlab-covid-19-scenarios
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strategy:
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fail-fast: true
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steps:
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- name: Checkout
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uses: actions/checkout@v1
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- name: Log into registry for Imperial images
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run: echo "${{ secrets.GITHUB_PAT }}" | docker login docker.pkg.github.com -u ${{ secrets.GITHUB_PAT_USER }} --password-stdin
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- name: Build image
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run: docker-compose build release
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- name: Log into registry
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run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login docker.pkg.github.com -u ${{ github.actor }} --password-stdin
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35+
- name: Push image (Local)
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run: |
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IMAGE_ID=docker.pkg.github.com/${{ github.repository }}/$IMAGE_NAME
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# Change all uppercase to lowercase
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IMAGE_ID=$(echo $IMAGE_ID | tr '[A-Z]' '[a-z]')
40+
# Strip git ref prefix from version
41+
VERSION=$(echo "${{ github.ref }}" | sed -e 's,.*/\(.*\),\1,')
42+
# Strip "v" prefix from tag name
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[[ "${{ github.ref }}" == "refs/tags/$PACKAGE_NAME"* ]] && VERSION=$(echo $VERSION | sed -e 's/^v//')
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# Always tag with git sha or version tag
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echo IMAGE_ID=$IMAGE_ID
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echo VERSION=$VERSION
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docker tag image $IMAGE_ID:$VERSION
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docker push $IMAGE_ID:$VERSION

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