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Merge remote-tracking branch 'upstream/develop' into develop
2 parents 9c2ec13 + 029bd80 commit dde6995

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‎.github/workflows/deploy.yml

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name: Deploy to production
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on:
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pull_request:
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branches:
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- releases/v1
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types:
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- opened
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- synchronize
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- reopened
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- closed
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env:
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# Required for action steebchen/kubectl
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KUBE_CONFIG_DATA: ${{ secrets.kubeconfig_data_prod }}
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jobs:
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show-changes:
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if: github.event.pull_request.state != 'closed'
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- uses: azure/setup-kubectl@v1
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with:
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version: v1.18.0
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- name: Get resource diffs
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run: |
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set -e
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comment_file=/tmp/k8s_diff.txt
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app_manifest=k8s/app.yaml
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prod_manifest_dir=k8s.prod
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test -e ~/.kube || mkdir ~/.kube
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cat <<EOF > ~/.kube/config
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$(printf '%s' "$KUBE_CONFIG_DATA" | base64 -d)
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EOF
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app_diff=$(kubectl diff -f $app_manifest || true)
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if [ -n "$app_diff" ]; then
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app_diff_msg=$(cat <<EOF
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To be applied to prod from $app_manifest:
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\`\`\`diff
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$app_diff
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\`\`\`
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EOF)
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fi
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prod_diff=$(kubectl diff -Rf $prod_manifest_dir || true)
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if [ -n "$prod_diff" ]; then
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prod_diff_msg=$(cat <<EOF
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To be applied to prod from $prod_manifest_dir:
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\`\`\`diff
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$prod_diff
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\`\`\`
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EOF)
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fi
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cat <<EOF > $comment_file
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$app_diff_msg
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$prod_diff_msg
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EOF
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- uses: actions/upload-artifact@v1
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with:
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name: comment
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path: /tmp/k8s_diff.txt
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- uses: actions/download-artifact@v1
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with:
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name: comment
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- name: Publish resource diffs
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uses: machine-learning-apps/[email protected]
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env:
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GITHUB_TOKEN: ${{ github.token }}
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with:
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path: comment/k8s_diff.txt
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deploy-prod:
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if: github.event.pull_request.merged
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- name: Deploy to prod
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uses: steebchen/[email protected]
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with:
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args: apply -f k8s/app.yaml
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- name: Sync prod resources
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uses: steebchen/[email protected]
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with:
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args: apply -Rf k8s.prod
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- name: Wait for deploy to complete
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uses: steebchen/[email protected]
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with:
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args: -n chime rollout status deployment.v1.apps/chime
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- name: Show completed deployment
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uses: steebchen/[email protected]
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with:
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args: -n chime get deployment chime -o yaml

‎.github/workflows/dockerpublish.yml

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env:
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IMAGE_NAME: penn-chime
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DEPLOY_PUSH_BRANCH: develop
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# Required for action steebchen/kubectl
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KUBE_CONFIG_DATA: ${{ secrets.kubeconfig_data_preprod }}
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jobs:
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# Run tests.
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docker tag image $IMAGE_ID:$VERSION
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docker push $IMAGE_ID:$VERSION
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deploy-preprod:
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needs: push
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if: github.event_name == 'push'
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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with:
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fetch-depth: 0 # Needed for proper rebase
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- name: Update application manifest
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run: |
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# Strip git ref prefix from version
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VERSION=$(echo "${{ github.ref }}" | sed -e 's,.*/\(.*\),\1,')
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# Strip "v" prefix from tag name
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[[ "${{ github.ref }}" == "refs/tags/"* ]] && VERSION=$(echo $VERSION | sed -e 's/^v//')
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# Pass version to subsequent steps
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echo "::set-env name=VERSION::$VERSION"
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# Update image version in application manifest
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sed -Ei "s,(- image: docker.pkg.github.com)(.*),\1/${GITHUB_REPOSITORY,,}/$IMAGE_NAME:$VERSION," k8s/app.yaml
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# Show updated manifest file
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cat k8s/app.yaml
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- name: Deploy to preprod
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uses: steebchen/[email protected]
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with:
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args: apply -f k8s/app.yaml
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- name: Sync preprod resources
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uses: steebchen/[email protected]
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with:
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args: apply -Rf k8s.preprod
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- name: Wait for deploy to complete
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uses: steebchen/[email protected]
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with:
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args: -n chime rollout status deployment.v1.apps/chime
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- name: Show completed deployment
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uses: steebchen/[email protected]
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with:
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args: -n chime get deployment chime -o yaml
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- name: Push manifest update
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uses: github-actions-x/[email protected]
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with:
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github-token: ${{ secrets.GITHUB_TOKEN }}
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push-branch: ${{ env.DEPLOY_PUSH_BRANCH }}
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commit-message: "chore: bump k8s manifest up CHIME ${{ env.VERSION }}"
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rebase: 'true'
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name: Chime CI
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email: [email protected]

‎.github/workflows/pythonapp.yml

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uses: cypress-io/[email protected]
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with:
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working-directory: e2e
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wait-on: 'http://localhost:8000'
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wait-on-timeout: 300
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‎Dockerfile.dash

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WORKDIR /code
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ARG PORT
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ENV PORT $PORT
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COPY requirements.txt requirements.txt
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RUN pip install -q -r requirements.txt
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RUN pip install -r requirements.txt
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COPY src src
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‎Pipfile.lock

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‎date_first_hospitalized.cfg

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--current-hospitalized 14
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--date-first-hospitalized 2020-03-07
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--hospitalized-los 7
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--hospitalized-rate 0.025
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--icu-los 9
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--icu-rate 0.0075
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--infectious-days 14
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--known-infected 510
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--market_share 0.15
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--n-days 60
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--population 4119405
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--relative-contact-rate 0.3
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--ventilated-los 10
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--ventilated-rate 0.005

‎docker-compose-dash.yml

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version: '3.1'
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services:
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app:
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build:
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context: .
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dockerfile: Dockerfile.dash
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args:
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- PORT=${PORT}
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restart: always
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ports:
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- "${PORT}:8000"

‎docs/SUMMARY.md

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- [Data Analysis](contributing/data-analysis.md)
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- [Operations Support](contributing/operations-support.md)
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- Operations
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- [Release Process](./operations/release-process.md)
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- [Preparing a new release](./operations/prepare-new-chime-release.md)
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- [Release Process](./operations/release=process.md)
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- [The `chime-live` Cluster](./operations/chime-live-cluster.md)
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- [Deploy to Heroku](./operations/heroku.md)
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- [Deploy with Chef Habitat](./operations/habitat.md)

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