TSPS-368 Update imputation_beagle to array_imputation #840
Workflow file for this run
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| name: Bump, Tag, Publish, and Deploy | |
| # The purpose of the workflow is to: | |
| # 1. Bump the version number and tag the release | |
| # 2. Build and publish the python client to PyPi | |
| # 3. Build and publish the client to Artifactory | |
| # 4. Build docker image and publish to GCR | |
| # 5. Trigger deployment to the dev environment | |
| # | |
| # When run on merge to main, it tags and bumps the patch version by default. You can | |
| # bump other parts of the version by putting #major, #minor, or #patch in your commit | |
| # message. | |
| # | |
| # When run on a hotfix branch, it tags and generates the hotfix version | |
| # | |
| # When run manually, you can specify the part of the semantic version to bump | |
| # | |
| # The workflow relies on github secrets: | |
| # - ARTIFACTORY_PASSWORD - password for publishing the client to artifactory | |
| # - ARTIFACTORY_USERNAME - username for publishing the client to artifactory | |
| # - BROADBOT_TOKEN - the broadbot token, so we can avoid two reviewer rule on GHA operations | |
| # - SLACK_WEBHOOK_URL - the webhook url to post to the desired Slack channel | |
| on: | |
| push: | |
| branches: | |
| - main | |
| paths-ignore: | |
| - 'README.md' | |
| - '.github/**' | |
| pull_request: | |
| workflow_dispatch: | |
| inputs: | |
| bump: | |
| description: 'Part of the version to bump: major, minor, patch' | |
| required: false | |
| default: 'patch' | |
| type: choice | |
| options: | |
| - patch | |
| - minor | |
| - major | |
| branch: | |
| description: 'Branch to run the workflow on' | |
| required: false | |
| default: 'main' | |
| env: | |
| SERVICE_NAME: ${{ github.event.repository.name }} | |
| IMAGE_NAME: ${{ github.event.repository.name }} | |
| GOOGLE_DOCKER_REPOSITORY: us-central1-docker.pkg.dev | |
| GOOGLE_PROJECT: dsp-artifact-registry | |
| jobs: | |
| bump-check: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| is-bump: ${{ steps.skiptest.outputs.is-bump }} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Skip version bump merges | |
| id: skiptest | |
| uses: ./.github/actions/bump-skip | |
| with: | |
| event-name: ${{ github.event_name }} | |
| tag-job: | |
| needs: [ bump-check ] | |
| runs-on: ubuntu-latest | |
| if: needs.bump-check.outputs.is-bump == 'no' | |
| outputs: | |
| tag: ${{ steps.tag.outputs.new_tag }} | |
| new-tag-for-python-client-version: ${{ steps.generate-params.outputs.new-tag-for-python-client-version }} | |
| checkout-ref: ${{ steps.generate-params.outputs.checkout-ref }} | |
| steps: | |
| - name: Set part of semantic version to bump | |
| id: controls | |
| run: | | |
| SEMVER_PART="" | |
| CHECKOUT_BRANCH="$GITHUB_REF" | |
| if ${{github.event_name == 'push' }}; then | |
| SEMVER_PART="patch" | |
| elif ${{github.event_name == 'workflow_dispatch' }}; then | |
| SEMVER_PART=${{ github.event.inputs.bump }} | |
| CHECKOUT_BRANCH=${{ github.event.inputs.branch }} | |
| fi | |
| echo ::set-output name=semver-part::$SEMVER_PART | |
| echo ::set-output name=checkout-branch::$CHECKOUT_BRANCH | |
| - name: Checkout current code | |
| uses: actions/checkout@v2 | |
| with: | |
| ref: ${{ steps.controls.outputs.checkout-branch }} | |
| token: ${{ secrets.BROADBOT_TOKEN }} | |
| - name: Bump the tag to a new version | |
| # https://github.com/DataBiosphere/github-actions/tree/master/actions/bumper | |
| uses: databiosphere/github-actions/actions/[email protected] | |
| id: tag | |
| env: | |
| DEFAULT_BUMP: patch | |
| GITHUB_TOKEN: ${{ secrets.BROADBOT_TOKEN }} | |
| HOTFIX_BRANCHES: hotfix.* | |
| OVERRIDE_BUMP: ${{ steps.controls.outputs.semver-part }} | |
| RELEASE_BRANCHES: main | |
| VERSION_FILE_PATH: settings.gradle | |
| VERSION_LINE_MATCH: "^gradle.ext.releaseVersion\\s*=\\s*\".*\"" | |
| VERSION_SUFFIX: SNAPSHOT | |
| - name: Generate tag for Java resources, version for Python, and checkout-ref to use in subsequent jobs | |
| id: generate-params | |
| run: | | |
| if [ ${{ github.event_name != 'pull_request' }} == true ]; then | |
| # This workflow was called on a push to main or manually, i.e. a PR merge / new release | |
| echo "New tag provided: ${{ steps.tag.outputs.new_tag }}" | |
| echo "Will use python client version based on tag: ${{ steps.tag.outputs.new_tag }}" | |
| echo "new-tag-for-python-client-version=${{ steps.tag.outputs.new_tag }}" >> $GITHUB_OUTPUT | |
| echo "Will use checkout-ref: ${{ steps.tag.outputs.new_tag }}" | |
| echo "checkout-ref=${{ steps.tag.outputs.new_tag }}" >> $GITHUB_OUTPUT | |
| else | |
| # This workflow was called on a PR, and the new tag was not actually created | |
| echo "New tag provided: ${{ steps.tag.outputs.new_tag }}" | |
| echo "Will use python client version '0.0.0'. This will not overwrite the existing PyPi version '0.0.0'" | |
| echo "new-tag-for-python-client-version='0.0.0'" >> $GITHUB_OUTPUT | |
| echo "Will use checkout-ref: $GITHUB_REF" | |
| echo "checkout-ref=$GITHUB_REF" >> $GITHUB_OUTPUT | |
| fi | |
| # Publish Python client to PyPI | |
| python-client-job: | |
| needs: [ tag-job ] | |
| uses: ./.github/workflows/release-python-client.yml | |
| with: | |
| new-tag-for-python-client-version: ${{ needs.tag-job.outputs.new-tag-for-python-client-version }} | |
| checkout-ref: ${{ needs.tag-job.outputs.checkout-ref }} | |
| # Publish the Java client to Artifactory and deploy the docker image to GCR | |
| publish-docker-deploy: | |
| needs: [ tag-job ] | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: 'write' | |
| id-token: 'write' | |
| steps: | |
| - name: Set up AdoptOpenJDK | |
| uses: actions/setup-java@v2 | |
| with: | |
| distribution: 'temurin' | |
| java-version: 17 | |
| - name: Checkout current code | |
| uses: actions/checkout@v2 | |
| with: | |
| ref: ${{ needs.tag-job.outputs.checkout-ref }} | |
| token: ${{ secrets.BROADBOT_TOKEN }} | |
| - name: Cache Gradle packages | |
| uses: actions/cache@v2 | |
| with: | |
| path: | | |
| ~/.gradle/caches | |
| ~/.gradle/wrapper | |
| key: v1-${{ runner.os }}-gradle-${{ hashfiles('**/gradle-wrapper.properties') }}-${{ hashFiles('**/*.gradle') }} | |
| restore-keys: v1-${{ runner.os }}-gradle-${{ hashfiles('**/gradle-wrapper.properties') }} | |
| - name: Grant execute permission for gradlew | |
| run: chmod +x gradlew | |
| # Publish Java client to artifactory | |
| - name: Publish Java client to Artifactory | |
| if: ${{ github.event_name != 'pull_request' }} | |
| run: ./gradlew :client:artifactoryPublish --scan | |
| env: | |
| ARTIFACTORY_USERNAME: ${{ secrets.ARTIFACTORY_USERNAME }} | |
| ARTIFACTORY_PASSWORD: ${{ secrets.ARTIFACTORY_PASSWORD }} | |
| ARTIFACTORY_REPO_KEY: "libs-snapshot-local" | |
| - name: Auth to GCP | |
| id: 'auth' | |
| uses: google-github-actions/auth@v0 | |
| with: | |
| token_format: 'access_token' | |
| workload_identity_provider: 'projects/1038484894585/locations/global/workloadIdentityPools/github-wi-pool/providers/github-wi-provider' | |
| service_account: 'dsp-artifact-registry-push@dsp-artifact-registry.iam.gserviceaccount.com' | |
| # Install gcloud, `setup-gcloud` automatically picks up authentication from `auth`. | |
| - name: 'Set up Cloud SDK' | |
| uses: 'google-github-actions/setup-gcloud@v0' | |
| - name: Explicitly auth Docker for Artifact Registry | |
| run: gcloud auth configure-docker $GOOGLE_DOCKER_REPOSITORY --quiet | |
| - name: Construct docker image name and tag | |
| id: image-name | |
| run: echo ::set-output name=name::${GOOGLE_DOCKER_REPOSITORY}/${GOOGLE_PROJECT}/${SERVICE_NAME}/${IMAGE_NAME}:${{ needs.tag-job.outputs.tag }} | |
| - name: Build image locally with jib | |
| run: | | |
| ./gradlew --build-cache :service:jibDockerBuild \ | |
| --image=${{ steps.image-name.outputs.name }} \ | |
| -Djib.console=plain | |
| - name: Push GCR image | |
| run: docker push ${{ steps.image-name.outputs.name }} | |
| - name: Make release | |
| if: ${{ github.event_name != 'pull_request' }} | |
| uses: ncipollo/release-action@v1 | |
| id: create_release | |
| with: | |
| tag: ${{ needs.tag-job.outputs.tag }} | |
| - name: Notify slack on failure | |
| uses: broadinstitute/[email protected] | |
| if: failure() | |
| env: | |
| SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK_URL }} | |
| with: | |
| channel: '#terra-tsps-alerts' | |
| status: failure | |
| author_name: Publish image | |
| fields: job | |
| text: 'Publish image failed :sadpanda: ${{ github.event.pull_request.html_url || github.event.head_commit.url }}' | |
| username: 'Terra Scientific Pipelines Service Action' | |
| report-to-sherlock: | |
| # Report new Teaspoons version to Broad DevOps | |
| uses: broadinstitute/sherlock/.github/workflows/client-report-app-version.yaml@main | |
| needs: [ bump-check, tag-job, publish-docker-deploy ] | |
| if: ${{ needs.bump-check.outputs.is-bump == 'no' }} | |
| with: | |
| new-version: ${{ needs.tag-job.outputs.tag }} | |
| chart-name: 'tsps' | |
| permissions: | |
| contents: 'read' | |
| id-token: 'write' | |
| set-version-in-dev: | |
| # Put new Teaspoons version in Broad dev environment | |
| uses: broadinstitute/sherlock/.github/workflows/client-set-environment-app-version.yaml@main | |
| needs: [ bump-check, tag-job, report-to-sherlock ] | |
| if: ${{ needs.bump-check.outputs.is-bump == 'no' && github.event_name != 'pull_request' }} | |
| with: | |
| new-version: ${{ needs.tag-job.outputs.tag }} | |
| chart-name: 'tsps' | |
| environment-name: 'dev' | |
| secrets: | |
| sync-git-token: ${{ secrets.BROADBOT_TOKEN }} | |
| permissions: | |
| id-token: 'write' |