LazyToolBox: clear _tool_versions_by_id + lineage on remove_tool_by_id #328
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| name: Build Container Image | |
| on: | |
| push: | |
| branches: | |
| - dev | |
| - release_* | |
| tags: | |
| - v* | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| ghcrbuild: | |
| name: Build container image for GHCR | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v6 | |
| with: | |
| persist-credentials: false | |
| # https://stackoverflow.com/questions/59810838/how-to-get-the-short-sha-for-the-github-workflow | |
| - name: Set outputs | |
| id: commit | |
| run: echo "sha_short=$(git rev-parse --short HEAD)" >> $GITHUB_OUTPUT | |
| - name: Set branch name | |
| id: branch | |
| run: | | |
| if [[ "$GITHUB_REF" == "refs/tags/"* ]]; then | |
| echo "name=${GITHUB_REF#refs/tags/v}" >> $GITHUB_OUTPUT | |
| elif [[ "$GITHUB_REF" == "refs/heads/dev" ]]; then | |
| echo "name=dev" >> $GITHUB_OUTPUT | |
| elif [[ "$GITHUB_REF" == "refs/heads/release_"* ]]; then | |
| echo "name=${GITHUB_REF#refs/heads/release_}-auto" >> $GITHUB_OUTPUT | |
| fi | |
| shell: bash | |
| - name: Extract metadata for container image | |
| id: meta | |
| uses: docker/metadata-action@v6 | |
| with: | |
| images: ghcr.io/${{ github.repository }} | |
| tags: | | |
| type=raw,value=${{steps.branch.outputs.name}} | |
| - name: Build args | |
| id: buildargs | |
| run: | | |
| echo "gitcommit=$(git rev-parse HEAD)" >> $GITHUB_OUTPUT | |
| echo "builddate=$(date -u +'%Y-%m-%dT%H:%M:%SZ')" >> $GITHUB_OUTPUT | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v4 | |
| with: | |
| platforms: linux/amd64 | |
| - name: Login to GHCR | |
| uses: docker/login-action@v4 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.repository_owner }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Build and push container image to ghcr | |
| uses: docker/build-push-action@v7 | |
| with: | |
| build-args: | | |
| GIT_COMMIT=${{ steps.buildargs.outputs.gitcommit }} | |
| BUILD_DATE=${{ steps.buildargs.outputs.builddate }} | |
| IMAGE_TAG=${{ steps.branch.outputs.name }} | |
| file: .k8s_ci.Dockerfile | |
| push: true | |
| context: . | |
| tags: ${{ steps.meta.outputs.tags }} | |
| labels: ${{ steps.meta.outputs.labels }} | |
| platforms: linux/amd64 | |
| build: | |
| name: Build container image for Galaxy repos | |
| runs-on: ubuntu-latest | |
| if: github.repository_owner == 'galaxyproject' | |
| outputs: | |
| tag: ${{ steps.branch.outputs.name }} | |
| version: ${{ steps.version.outputs.version }} | |
| steps: | |
| - uses: actions/checkout@v6 | |
| with: | |
| persist-credentials: false | |
| - uses: actions/setup-python@v6 | |
| with: | |
| python-version: '3.12' | |
| # https://stackoverflow.com/questions/59810838/how-to-get-the-short-sha-for-the-github-workflow | |
| - name: Set outputs | |
| id: commit | |
| run: echo "sha_short=$(git rev-parse --short HEAD)" >> $GITHUB_OUTPUT | |
| - name: Set branch name | |
| id: branch | |
| run: | | |
| if [[ "$GITHUB_REF" == "refs/tags/"* ]]; then | |
| echo "name=${GITHUB_REF#refs/tags/v}" >> $GITHUB_OUTPUT | |
| elif [[ "$GITHUB_REF" == "refs/heads/dev" ]]; then | |
| echo "name=dev" >> $GITHUB_OUTPUT | |
| elif [[ "$GITHUB_REF" == "refs/heads/release_"* ]]; then | |
| echo "name=${GITHUB_REF#refs/heads/release_}-auto" >> $GITHUB_OUTPUT | |
| fi | |
| shell: bash | |
| - name: Get the current Galaxy version | |
| id: version | |
| run: | | |
| version=$(PYTHONPATH=lib python3 -c "from galaxy.version import VERSION; print(VERSION)") | |
| echo "version=$version" >> $GITHUB_OUTPUT | |
| - name: Build args | |
| id: buildargs | |
| run: | | |
| echo "gitcommit=$(git rev-parse HEAD)" >> $GITHUB_OUTPUT | |
| echo "builddate=$(date -u +'%Y-%m-%dT%H:%M:%SZ')" >> $GITHUB_OUTPUT | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v4 | |
| - name: Login to quay.io | |
| uses: docker/login-action@v4 | |
| with: | |
| registry: quay.io | |
| username: ${{ secrets.QUAY_USERNAME }} | |
| password: ${{ secrets.QUAY_PASSWORD }} | |
| - name: Login to DockerHub | |
| uses: docker/login-action@v4 | |
| with: | |
| username: ${{ secrets.DOCKERHUB_USERNAME }} | |
| password: ${{ secrets.DOCKERHUB_PASSWORD }} | |
| - name: Build and push galaxy-min image | |
| uses: docker/build-push-action@v7 | |
| with: | |
| context: . | |
| file: .k8s_ci.Dockerfile | |
| push: true | |
| build-args: | | |
| GIT_COMMIT=${{ steps.buildargs.outputs.gitcommit }} | |
| BUILD_DATE=${{ steps.buildargs.outputs.builddate }} | |
| IMAGE_TAG=${{ steps.branch.outputs.name }} | |
| tags: | | |
| galaxy/galaxy-min:${{ steps.branch.outputs.name }} | |
| quay.io/galaxyproject/galaxy-min:${{ steps.branch.outputs.name }} | |
| - name: Create Dockerfile for auto-expiring image | |
| run: echo "FROM galaxy/galaxy-min:${{ steps.branch.outputs.name }}" > /tmp/Dockerfile.auto | |
| - name: Build and push auto-expiring per-commit image | |
| uses: docker/build-push-action@v7 | |
| with: | |
| file: /tmp/Dockerfile.auto | |
| push: true | |
| tags: quay.io/galaxyproject/galaxy-k8s-auto:${{ steps.commit.outputs.sha_short }} | |
| labels: quay.expires-after=90d | |
| smoke-test: | |
| name: Try installing the new image | |
| runs-on: ubuntu-latest | |
| needs: [ build ] | |
| steps: | |
| - name: Start k8s locally | |
| uses: jupyterhub/action-k3s-helm@v4 | |
| with: | |
| k3s-version: v1.32.0+k3s1 # releases: https://github.com/k3s-io/k3s/tags | |
| metrics-enabled: false | |
| traefik-enabled: false | |
| - name: Verify function of k8s, kubectl, and helm | |
| run: | | |
| echo "kubeconfig: $KUBECONFIG" | |
| kubectl version | |
| kubectl get pods --all-namespaces | |
| helm version | |
| helm list | |
| - name: Add the Galaxy Helm repository | |
| run: helm repo add galaxy https://github.com/CloudVE/helm-charts/raw/master | |
| - name: Install the Galaxy dependencies | |
| run: | | |
| helm install galaxy-deps galaxy/galaxy-deps \ | |
| --namespace galaxy-deps \ | |
| --create-namespace \ | |
| --set cvmfs.cvmfscsi.cache.alien.enabled=false \ | |
| --wait \ | |
| --timeout=1200s | |
| - name: Install Galaxy using the image we just pushed | |
| run: | | |
| helm install galaxy galaxy/galaxy \ | |
| --namespace galaxy \ | |
| --create-namespace \ | |
| --set persistence.accessMode="ReadWriteOnce" \ | |
| --set resources.requests.memory=0Mi,resources.requests.cpu=0m \ | |
| --set image.tag=${{ needs.build.outputs.tag }} \ | |
| --wait \ | |
| --timeout=1200s | |
| - name: Debug deployment on failure | |
| if: failure() | |
| run: | | |
| echo "=== Deployment failed, gathering debug information ===" | |
| echo "=== All pods in galaxy namespace ===" | |
| kubectl get pods -n galaxy -o wide | |
| echo "=== All pods in galaxy-deps namespace ===" | |
| kubectl get pods -n galaxy-deps -o wide | |
| echo "=== CSI Drivers ===" | |
| kubectl get csidriver | |
| echo "=== Storage Classes ===" | |
| kubectl get sc | |
| echo "=== PVCs in galaxy namespace ===" | |
| kubectl get pvc -n galaxy | |
| echo "=== PVCs in galaxy-deps namespace ===" | |
| kubectl get pvc -n galaxy-deps | |
| echo "=== Recent events in galaxy namespace ===" | |
| kubectl get events -n galaxy --sort-by='.lastTimestamp' | tail -50 | |
| echo "=== Recent events in galaxy-deps namespace ===" | |
| kubectl get events -n galaxy-deps --sort-by='.lastTimestamp' | tail -50 | |
| echo "=== Describe pending/failed pods in galaxy namespace ===" | |
| for pod in $(kubectl get pods -n galaxy --field-selector=status.phase!=Running,status.phase!=Succeeded -o name 2>/dev/null); do | |
| echo "--- Describing $pod ---" | |
| kubectl describe -n galaxy $pod | |
| done | |
| echo "=== Describe pending/failed pods in galaxy-deps namespace ===" | |
| for pod in $(kubectl get pods -n galaxy-deps --field-selector=status.phase!=Running,status.phase!=Succeeded -o name 2>/dev/null); do | |
| echo "--- Describing $pod ---" | |
| kubectl describe -n galaxy-deps $pod | |
| done | |
| - name: Check the version | |
| run: | | |
| kubectl get svc -n galaxy | |
| kubectl describe svc -n galaxy galaxy-nginx | |
| address=$(kubectl get svc -n galaxy galaxy-nginx -o jsonpath="http://{.spec.clusterIP}:{.spec.ports[0].port}/galaxy/api/version") | |
| echo "Address is $address" | |
| appVersion=${{ needs.build.outputs.version }} | |
| apiVersion=$(curl $address | jq -r '"\(.version_major).\(.version_minor)"') | |
| echo "appVersion: $appVersion" | |
| echo "apiVersion: $apiVersion" | |
| if [ "$appVersion" != "$apiVersion" ]; then | |
| exit 1 | |
| fi | |
| - name: Check client build is served | |
| run: | | |
| base_url=$(kubectl get svc -n galaxy galaxy-nginx -o jsonpath="http://{.spec.clusterIP}:{.spec.ports[0].port}") | |
| css_url="${base_url}/galaxy/static/dist/base.css" | |
| echo "Checking client build at $css_url" | |
| status_code=$(curl -s -o /dev/null -w "%{http_code}" "$css_url") | |
| echo "Status code: $status_code" | |
| if [ "$status_code" != "200" ]; then | |
| echo "ERROR: Failed to fetch base.css (status: $status_code)" | |
| echo "This indicates the client build was not properly included in the image" | |
| exit 1 | |
| fi | |
| echo "Client build is properly served" | |
| pr: | |
| name: Create a PR to update the Galaxy Helm chart when a release is tagged | |
| runs-on: ubuntu-latest | |
| needs: [smoke-test, build] | |
| if: startsWith(github.ref, 'refs/tags/') | |
| steps: | |
| - name: Checkout Galaxy Helm chart | |
| uses: actions/checkout@v6 | |
| with: | |
| repository: galaxyproject/galaxy-helm | |
| persist-credentials: false | |
| - name: Update Chart.yaml appVersion | |
| run: | | |
| sed -i "s/^appVersion:.*/appVersion: \"${{ needs.build.outputs.version }}\"/" galaxy/Chart.yaml | |
| - name: Update values.yaml image.tag | |
| run: | | |
| sed -i "s/^ tag:.*/ tag: \"${{ needs.build.outputs.tag }}\"/" galaxy/values.yaml | |
| - name: Create Pull Request | |
| uses: peter-evans/create-pull-request@v8 | |
| with: | |
| token: ${{ secrets.GALAXY_HELM_PULL_REQUEST_TOKEN }} | |
| commit-message: "Update Galaxy to version ${{ needs.build.outputs.version }}" | |
| title: "Update Galaxy to version ${{ needs.build.outputs.version }}" | |
| body: | | |
| This PR updates the Galaxy Helm chart to use the new Galaxy release. | |
| Changes: | |
| - appVersion: ${{ needs.build.outputs.version }} | |
| - image.tag: ${{ needs.build.outputs.tag }} | |
| Triggered by: ${{ github.ref }} | |
| branch: update-galaxy-${{ needs.build.outputs.version }} | |
| delete-branch: true | |
| labels: patch | |
| notify-failure: | |
| name: Notify Slack on failure | |
| runs-on: ubuntu-latest | |
| needs: [build, smoke-test] | |
| if: ${{ always() && (needs.build.result == 'failure' || needs.smoke-test.result == 'failure') }} | |
| steps: | |
| - name: Determine which job failed | |
| id: failure-info | |
| run: | | |
| if [[ "${{ needs.build.result }}" == "failure" ]]; then | |
| echo "failed_job=Docker image build" >> $GITHUB_OUTPUT | |
| elif [[ "${{ needs.smoke-test.result }}" == "failure" ]]; then | |
| echo "failed_job=Smoke test" >> $GITHUB_OUTPUT | |
| fi | |
| - name: Send Slack notification | |
| uses: slackapi/slack-github-action@v3.0.2 | |
| with: | |
| webhook: ${{ secrets.K8S_SLACK_WEBHOOK_URL }} | |
| webhook-type: incoming-webhook | |
| payload: | | |
| { | |
| "text": ":x: *Build Container Image Failed*", | |
| "blocks": [ | |
| { | |
| "type": "header", | |
| "text": { | |
| "type": "plain_text", | |
| "text": ":x: Build Container Image Failed", | |
| "emoji": true | |
| } | |
| }, | |
| { | |
| "type": "section", | |
| "fields": [ | |
| { | |
| "type": "mrkdwn", | |
| "text": "*Repository:*\n${{ github.repository }}" | |
| }, | |
| { | |
| "type": "mrkdwn", | |
| "text": "*Branch/Tag:*\n${{ github.ref_name }}" | |
| }, | |
| { | |
| "type": "mrkdwn", | |
| "text": "*Failed Job:*\n${{ steps.failure-info.outputs.failed_job }}" | |
| }, | |
| { | |
| "type": "mrkdwn", | |
| "text": "*Triggered by:*\n${{ github.actor }}" | |
| } | |
| ] | |
| }, | |
| { | |
| "type": "actions", | |
| "elements": [ | |
| { | |
| "type": "button", | |
| "text": { | |
| "type": "plain_text", | |
| "text": "View Workflow Run", | |
| "emoji": true | |
| }, | |
| "url": "${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}" | |
| } | |
| ] | |
| } | |
| ] | |
| } |